A new approach to compute accurate velocity of meteors
NASA Astrophysics Data System (ADS)
Egal, Auriane; Gural, Peter; Vaubaillon, Jeremie; Colas, Francois; Thuillot, William
2016-10-01
The CABERNET project was designed to push the limits of meteoroid orbit measurements by improving the determination of the meteors' velocities. Indeed, despite of the development of the cameras networks dedicated to the observation of meteors, there is still an important discrepancy between the measured orbits of meteoroids computed and the theoretical results. The gap between the observed and theoretic semi-major axis of the orbits is especially significant; an accurate determination of the orbits of meteoroids therefore largely depends on the computation of the pre-atmospheric velocities. It is then imperative to dig out how to increase the precision of the measurements of the velocity.In this work, we perform an analysis of different methods currently used to compute the velocities and trajectories of the meteors. They are based on the intersecting planes method developed by Ceplecha (1987), the least squares method of Borovicka (1990), and the multi-parameter fitting (MPF) method published by Gural (2012).In order to objectively compare the performances of these techniques, we have simulated realistic meteors ('fakeors') reproducing the different error measurements of many cameras networks. Some fakeors are built following the propagation models studied by Gural (2012), and others created by numerical integrations using the Borovicka et al. 2007 model. Different optimization techniques have also been investigated in order to pick the most suitable one to solve the MPF, and the influence of the geometry of the trajectory on the result is also presented.We will present here the results of an improved implementation of the multi-parameter fitting that allow an accurate orbit computation of meteors with CABERNET. The comparison of different velocities computation seems to show that if the MPF is by far the best method to solve the trajectory and the velocity of a meteor, the ill-conditioning of the costs functions used can lead to large estimate errors for noisy
Chen, W M; Deng, H W
2001-07-01
Transmission disequilibrium test (TDT) is a nuclear family-based analysis that can test linkage in the presence of association. It has gained extensive attention in theoretical investigation and in practical application; in both cases, the accuracy and generality of the power computation of the TDT are crucial. Despite extensive investigations, previous approaches for computing the statistical power of the TDT are neither accurate nor general. In this paper, we develop a general and highly accurate approach to analytically compute the power of the TDT. We compare the results from our approach with those from several other recent papers, all against the results obtained from computer simulations. We show that the results computed from our approach are more accurate than or at least the same as those from other approaches. More importantly, our approach can handle various situations, which include (1) families that consist of one or more children and that have any configuration of affected and nonaffected sibs; (2) families ascertained through the affection status of parent(s); (3) any mixed sample with different types of families in (1) and (2); (4) the marker locus is not a disease susceptibility locus; and (5) existence of allelic heterogeneity. We implement this approach in a user-friendly computer program: TDT Power Calculator. Its applications are demonstrated. The approach and the program developed here should be significant for theoreticians to accurately investigate the statistical power of the TDT in various situations, and for empirical geneticists to plan efficient studies using the TDT.
Mehmani, Yashar; Oostrom, Martinus; Balhoff, Matthew
2014-03-20
Several approaches have been developed in the literature for solving flow and transport at the pore-scale. Some authors use a direct modeling approach where the fundamental flow and transport equations are solved on the actual pore-space geometry. Such direct modeling, while very accurate, comes at a great computational cost. Network models are computationally more efficient because the pore-space morphology is approximated. Typically, a mixed cell method (MCM) is employed for solving the flow and transport system which assumes pore-level perfect mixing. This assumption is invalid at moderate to high Peclet regimes. In this work, a novel Eulerian perspective on modeling flow and transport at the pore-scale is developed. The new streamline splitting method (SSM) allows for circumventing the pore-level perfect mixing assumption, while maintaining the computational efficiency of pore-network models. SSM was verified with direct simulations and excellent matches were obtained against micromodel experiments across a wide range of pore-structure and fluid-flow parameters. The increase in the computational cost from MCM to SSM is shown to be minimal, while the accuracy of SSM is much higher than that of MCM and comparable to direct modeling approaches. Therefore, SSM can be regarded as an appropriate balance between incorporating detailed physics and controlling computational cost. The truly predictive capability of the model allows for the study of pore-level interactions of fluid flow and transport in different porous materials. In this paper, we apply SSM and MCM to study the effects of pore-level mixing on transverse dispersion in 3D disordered granular media.
Accurate modeling of parallel scientific computations
NASA Technical Reports Server (NTRS)
Nicol, David M.; Townsend, James C.
1988-01-01
Scientific codes are usually parallelized by partitioning a grid among processors. To achieve top performance it is necessary to partition the grid so as to balance workload and minimize communication/synchronization costs. This problem is particularly acute when the grid is irregular, changes over the course of the computation, and is not known until load time. Critical mapping and remapping decisions rest on the ability to accurately predict performance, given a description of a grid and its partition. This paper discusses one approach to this problem, and illustrates its use on a one-dimensional fluids code. The models constructed are shown to be accurate, and are used to find optimal remapping schedules.
NASA Astrophysics Data System (ADS)
Wiktor, Julia; Jomard, Gérald; Torrent, Marc
2015-09-01
Many techniques have been developed in the past in order to compute positron lifetimes in materials from first principles. However, there is still a lack of a fast and accurate self-consistent scheme that could handle accurately the forces acting on the ions induced by the presence of the positron. We will show in this paper that we have reached this goal by developing the two-component density functional theory within the projector augmented-wave (PAW) method in the open-source code abinit. This tool offers the accuracy of the all-electron methods with the computational efficiency of the plane-wave ones. We can thus deal with supercells that contain few hundreds to thousands of atoms to study point defects as well as more extended defects clusters. Moreover, using the PAW basis set allows us to use techniques able to, for instance, treat strongly correlated systems or spin-orbit coupling, which are necessary to study heavy elements, such as the actinides or their compounds.
Accurate paleointensities - the multi-method approach
NASA Astrophysics Data System (ADS)
de Groot, Lennart
2016-04-01
The accuracy of models describing rapid changes in the geomagnetic field over the past millennia critically depends on the availability of reliable paleointensity estimates. Over the past decade methods to derive paleointensities from lavas (the only recorder of the geomagnetic field that is available all over the globe and through geologic times) have seen significant improvements and various alternative techniques were proposed. The 'classical' Thellier-style approach was optimized and selection criteria were defined in the 'Standard Paleointensity Definitions' (Paterson et al, 2014). The Multispecimen approach was validated and the importance of additional tests and criteria to assess Multispecimen results must be emphasized. Recently, a non-heating, relative paleointensity technique was proposed -the pseudo-Thellier protocol- which shows great potential in both accuracy and efficiency, but currently lacks a solid theoretical underpinning. Here I present work using all three of the aforementioned paleointensity methods on suites of young lavas taken from the volcanic islands of Hawaii, La Palma, Gran Canaria, Tenerife, and Terceira. Many of the sampled cooling units are <100 years old, the actual field strength at the time of cooling is therefore reasonably well known. Rather intuitively, flows that produce coherent results from two or more different paleointensity methods yield the most accurate estimates of the paleofield. Furthermore, the results for some flows pass the selection criteria for one method, but fail in other techniques. Scrutinizing and combing all acceptable results yielded reliable paleointensity estimates for 60-70% of all sampled cooling units - an exceptionally high success rate. This 'multi-method paleointensity approach' therefore has high potential to provide the much-needed paleointensities to improve geomagnetic field models for the Holocene.
Accurate atom-mapping computation for biochemical reactions.
Latendresse, Mario; Malerich, Jeremiah P; Travers, Mike; Karp, Peter D
2012-11-26
The complete atom mapping of a chemical reaction is a bijection of the reactant atoms to the product atoms that specifies the terminus of each reactant atom. Atom mapping of biochemical reactions is useful for many applications of systems biology, in particular for metabolic engineering where synthesizing new biochemical pathways has to take into account for the number of carbon atoms from a source compound that are conserved in the synthesis of a target compound. Rapid, accurate computation of the atom mapping(s) of a biochemical reaction remains elusive despite significant work on this topic. In particular, past researchers did not validate the accuracy of mapping algorithms. We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric. The metric is based on bond propensity to react and computes biochemically valid atom mappings for a large percentage of biochemical reactions. MWED models can be formulated efficiently as Mixed-Integer Linear Programs (MILPs). We have demonstrated this approach on 7501 reactions of the MetaCyc database for which 87% of the models could be solved in less than 10 s. For 2.1% of the reactions, we found multiple optimal atom mappings. We show that the error rate is 0.9% (22 reactions) by comparing these atom mappings to 2446 atom mappings of the manually curated Kyoto Encyclopedia of Genes and Genomes (KEGG) RPAIR database. To our knowledge, our computational atom-mapping approach is the most accurate and among the fastest published to date. The atom-mapping data will be available in the MetaCyc database later in 2012; the atom-mapping software will be available within the Pathway Tools software later in 2012.
ERIC Educational Resources Information Center
Harbusch, Karin; Itsova, Gergana; Koch, Ulrich; Kuhner, Christine
2009-01-01
We built a natural language processing (NLP) system implementing a "virtual writing conference" for elementary-school children, with German as the target language. Currently, state-of-the-art computer support for writing tasks is restricted to multiple-choice questions or quizzes because automatic parsing of the often ambiguous and fragmentary…
Photoacoustic computed tomography without accurate ultrasonic transducer responses
NASA Astrophysics Data System (ADS)
Sheng, Qiwei; Wang, Kun; Xia, Jun; Zhu, Liren; Wang, Lihong V.; Anastasio, Mark A.
2015-03-01
Conventional photoacoustic computed tomography (PACT) image reconstruction methods assume that the object and surrounding medium are described by a constant speed-of-sound (SOS) value. In order to accurately recover fine structures, SOS heterogeneities should be quantified and compensated for during PACT reconstruction. To address this problem, several groups have proposed hybrid systems that combine PACT with ultrasound computed tomography (USCT). In such systems, a SOS map is reconstructed first via USCT. Consequently, this SOS map is employed to inform the PACT reconstruction method. Additionally, the SOS map can provide structural information regarding tissue, which is complementary to the functional information from the PACT image. We propose a paradigm shift in the way that images are reconstructed in hybrid PACT-USCT imaging. Inspired by our observation that information about the SOS distribution is encoded in PACT measurements, we propose to jointly reconstruct the absorbed optical energy density and SOS distributions from a combined set of USCT and PACT measurements, thereby reducing the two reconstruction problems into one. This innovative approach has several advantages over conventional approaches in which PACT and USCT images are reconstructed independently: (1) Variations in the SOS will automatically be accounted for, optimizing PACT image quality; (2) The reconstructed PACT and USCT images will possess minimal systematic artifacts because errors in the imaging models will be optimally balanced during the joint reconstruction; (3) Due to the exploitation of information regarding the SOS distribution in the full-view PACT data, our approach will permit high-resolution reconstruction of the SOS distribution from sparse array data.
Highly Accurate Inverse Consistent Registration: A Robust Approach
Reuter, Martin; Rosas, H. Diana; Fischl, Bruce
2010-01-01
The registration of images is a task that is at the core of many applications in computer vision. In computational neuroimaging where the automated segmentation of brain structures is frequently used to quantify change, a highly accurate registration is necessary for motion correction of images taken in the same session, or across time in longitudinal studies where changes in the images can be expected. This paper, inspired by Nestares and Heeger (2000), presents a method based on robust statistics to register images in the presence of differences, such as jaw movement, differential MR distortions and true anatomical change. The approach we present guarantees inverse consistency (symmetry), can deal with different intensity scales and automatically estimates a sensitivity parameter to detect outlier regions in the images. The resulting registrations are highly accurate due to their ability to ignore outlier regions and show superior robustness with respect to noise, to intensity scaling and outliers when compared to state-of-the-art registration tools such as FLIRT (in FSL) or the coregistration tool in SPM. PMID:20637289
Measurement of Fracture Geometry for Accurate Computation of Hydraulic Conductivity
NASA Astrophysics Data System (ADS)
Chae, B.; Ichikawa, Y.; Kim, Y.
2003-12-01
Fluid flow in rock mass is controlled by geometry of fractures which is mainly characterized by roughness, aperture and orientation. Fracture roughness and aperture was observed by a new confocal laser scanning microscope (CLSM; Olympus OLS1100). The wavelength of laser is 488nm, and the laser scanning is managed by a light polarization method using two galvano-meter scanner mirrors. The system improves resolution in the light axis (namely z) direction because of the confocal optics. The sampling is managed in a spacing 2.5 μ m along x and y directions. The highest measurement resolution of z direction is 0.05 μ m, which is the more accurate than other methods. For the roughness measurements, core specimens of coarse and fine grained granites were provided. Measurements were performed along three scan lines on each fracture surface. The measured data were represented as 2-D and 3-D digital images showing detailed features of roughness. Spectral analyses by the fast Fourier transform (FFT) were performed to characterize on the roughness data quantitatively and to identify influential frequency of roughness. The FFT results showed that components of low frequencies were dominant in the fracture roughness. This study also verifies that spectral analysis is a good approach to understand complicate characteristics of fracture roughness. For the aperture measurements, digital images of the aperture were acquired under applying five stages of uniaxial normal stresses. This method can characterize the response of aperture directly using the same specimen. Results of measurements show that reduction values of aperture are different at each part due to rough geometry of fracture walls. Laboratory permeability tests were also conducted to evaluate changes of hydraulic conductivities related to aperture variation due to different stress levels. The results showed non-uniform reduction of hydraulic conductivity under increase of the normal stress and different values of
Neutron supermirrors: an accurate theory for layer thickness computation
NASA Astrophysics Data System (ADS)
Bray, Michael
2001-11-01
We present a new theory for the computation of Super-Mirror stacks, using accurate formulas derived from the classical optics field. Approximations are introduced into the computation, but at a later stage than existing theories, providing a more rigorous treatment of the problem. The final result is a continuous thickness stack, whose properties can be determined at the outset of the design. We find that the well-known fourth power dependence of number of layers versus maximum angle is (of course) asymptotically correct. We find a formula giving directly the relation between desired reflectance, maximum angle, and number of layers (for a given pair of materials). Note: The author of this article, a classical opticist, has limited knowledge of the Neutron world, and begs forgiveness for any shortcomings, erroneous assumptions and/or misinterpretation of previous authors' work on the subject.
Direct computation of parameters for accurate polarizable force fields
Verstraelen, Toon Vandenbrande, Steven; Ayers, Paul W.
2014-11-21
We present an improved electronic linear response model to incorporate polarization and charge-transfer effects in polarizable force fields. This model is a generalization of the Atom-Condensed Kohn-Sham Density Functional Theory (DFT), approximated to second order (ACKS2): it can now be defined with any underlying variational theory (next to KS-DFT) and it can include atomic multipoles and off-center basis functions. Parameters in this model are computed efficiently as expectation values of an electronic wavefunction, obviating the need for their calibration, regularization, and manual tuning. In the limit of a complete density and potential basis set in the ACKS2 model, the linear response properties of the underlying theory for a given molecular geometry are reproduced exactly. A numerical validation with a test set of 110 molecules shows that very accurate models can already be obtained with fluctuating charges and dipoles. These features greatly facilitate the development of polarizable force fields.
An Accurate and Dynamic Computer Graphics Muscle Model
NASA Technical Reports Server (NTRS)
Levine, David Asher
1997-01-01
A computer based musculo-skeletal model was developed at the University in the departments of Mechanical and Biomedical Engineering. This model accurately represents human shoulder kinematics. The result of this model is the graphical display of bones moving through an appropriate range of motion based on inputs of EMGs and external forces. The need existed to incorporate a geometric muscle model in the larger musculo-skeletal model. Previous muscle models did not accurately represent muscle geometries, nor did they account for the kinematics of tendons. This thesis covers the creation of a new muscle model for use in the above musculo-skeletal model. This muscle model was based on anatomical data from the Visible Human Project (VHP) cadaver study. Two-dimensional digital images from the VHP were analyzed and reconstructed to recreate the three-dimensional muscle geometries. The recreated geometries were smoothed, reduced, and sliced to form data files defining the surfaces of each muscle. The muscle modeling function opened these files during run-time and recreated the muscle surface. The modeling function applied constant volume limitations to the muscle and constant geometry limitations to the tendons.
Computational vaccinology: quantitative approaches.
Flower, Darren R; McSparron, Helen; Blythe, Martin J; Zygouri, Christianna; Taylor, Debra; Guan, Pingping; Wan, Shouzhan; Coveney, Peter V; Walshe, Valerie; Borrow, Persephone; Doytchinova, Irini A
2003-01-01
The immune system is hierarchical and has many levels, exhibiting much emergent behaviour. However, at its heart are molecular recognition events that are indistinguishable from other types of biomacromolecular interaction. These can be addressed well by quantitative experimental and theoretical biophysical techniques, and particularly by methods from drug design. We review here our approach to computational immunovaccinology. In particular, we describe the JenPep database and two new techniques for T cell epitope prediction. One is based on quantitative structure-activity relationships (a 3D-QSAR method based on CoMSIA and another 2D method based on the Free-Wilson approach) and the other on atomistic molecular dynamic simulations using high performance computing. JenPep (http://www.jenner.ar.uk/ JenPep) is a relational database system supporting quantitative data on peptide binding to major histocompatibility complexes, TAP transporters, TCR-pMHC complexes, and an annotated list of B cell and T cell epitopes. Our 2D-QSAR method factors the contribution to peptide binding from individual amino acids as well as 1-2 and 1-3 residue interactions. In the 3D-QSAR approach, the influence of five physicochemical properties (volume, electrostatic potential, hydrophobicity, hydrogen-bond donor and acceptor abilities) on peptide affinity were considered. Both methods are exemplified through their application to the well-studied problem of peptide binding to the human class I MHC molecule HLA-A*0201. PMID:14712934
Madebene, Bruno; Ulusoy, Inga; Mancera, Luis; Scribano, Yohann; Chulkov, Sergey
2011-01-01
Summary We present a theoretical framework for the computation of anharmonic vibrational frequencies for large systems, with a particular focus on determining adsorbate frequencies from first principles. We give a detailed account of our local implementation of the vibrational self-consistent field approach and its correlation corrections. We show that our approach is both robust, accurate and can be easily deployed on computational grids in order to provide an efficient computational tool. We also present results on the vibrational spectrum of hydrogen fluoride on pyrene, on the thiophene molecule in the gas phase, and on small neutral gold clusters. PMID:22003450
Automated Development of Accurate Algorithms and Efficient Codes for Computational Aeroacoustics
NASA Technical Reports Server (NTRS)
Goodrich, John W.; Dyson, Rodger W.
1999-01-01
The simulation of sound generation and propagation in three space dimensions with realistic aircraft components is a very large time dependent computation with fine details. Simulations in open domains with embedded objects require accurate and robust algorithms for propagation, for artificial inflow and outflow boundaries, and for the definition of geometrically complex objects. The development, implementation, and validation of methods for solving these demanding problems is being done to support the NASA pillar goals for reducing aircraft noise levels. Our goal is to provide algorithms which are sufficiently accurate and efficient to produce usable results rapidly enough to allow design engineers to study the effects on sound levels of design changes in propulsion systems, and in the integration of propulsion systems with airframes. There is a lack of design tools for these purposes at this time. Our technical approach to this problem combines the development of new, algorithms with the use of Mathematica and Unix utilities to automate the algorithm development, code implementation, and validation. We use explicit methods to ensure effective implementation by domain decomposition for SPMD parallel computing. There are several orders of magnitude difference in the computational efficiencies of the algorithms which we have considered. We currently have new artificial inflow and outflow boundary conditions that are stable, accurate, and unobtrusive, with implementations that match the accuracy and efficiency of the propagation methods. The artificial numerical boundary treatments have been proven to have solutions which converge to the full open domain problems, so that the error from the boundary treatments can be driven as low as is required. The purpose of this paper is to briefly present a method for developing highly accurate algorithms for computational aeroacoustics, the use of computer automation in this process, and a brief survey of the algorithms that
Accurate Anharmonic IR Spectra from Integrated Cc/dft Approach
NASA Astrophysics Data System (ADS)
Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Carnimeo, Ivan; Puzzarini, Cristina
2014-06-01
The recent implementation of the computation of infrared (IR) intensities beyond the double harmonic approximation [1] paved the route to routine calculations of infrared spectra for a wide set of molecular systems. Contrary to common beliefs, second-order perturbation theory is able to deliver results of high accuracy provided that anharmonic resonances are properly managed [1,2]. It has been already shown for several small closed- and open shell molecular systems that the differences between coupled cluster (CC) and DFT anharmonic wavenumbers are mainly due to the harmonic terms, paving the route to introduce effective yet accurate hybrid CC/DFT schemes [2]. In this work we present that hybrid CC/DFT models can be applied also to the IR intensities leading to the simulation of highly accurate fully anharmonic IR spectra for medium-size molecules, including ones of atmospheric interest, showing in all cases good agreement with experiment even in the spectral ranges where non-fundamental transitions are predominant[3]. [1] J. Bloino and V. Barone, J. Chem. Phys. 136, 124108 (2012) [2] V. Barone, M. Biczysko, J. Bloino, Phys. Chem. Chem. Phys., 16, 1759-1787 (2014) [3] I. Carnimeo, C. Puzzarini, N. Tasinato, P. Stoppa, A. P. Charmet, M. Biczysko, C. Cappelli and V. Barone, J. Chem. Phys., 139, 074310 (2013)
Accurately measuring MPI broadcasts in a computational grid
Karonis N T; de Supinski, B R
1999-05-06
An MPI library's implementation of broadcast communication can significantly affect the performance of applications built with that library. In order to choose between similar implementations or to evaluate available libraries, accurate measurements of broadcast performance are required. As we demonstrate, existing methods for measuring broadcast performance are either inaccurate or inadequate. Fortunately, we have designed an accurate method for measuring broadcast performance, even in a challenging grid environment. Measuring broadcast performance is not easy. Simply sending one broadcast after another allows them to proceed through the network concurrently, thus resulting in inaccurate per broadcast timings. Existing methods either fail to eliminate this pipelining effect or eliminate it by introducing overheads that are as difficult to measure as the performance of the broadcast itself. This problem becomes even more challenging in grid environments. Latencies a long different links can vary significantly. Thus, an algorithm's performance is difficult to predict from it's communication pattern. Even when accurate pre-diction is possible, the pattern is often unknown. Our method introduces a measurable overhead to eliminate the pipelining effect, regardless of variations in link latencies. choose between different available implementations. Also, accurate and complete measurements could guide use of a given implementation to improve application performance. These choices will become even more important as grid-enabled MPI libraries [6, 7] become more common since bad choices are likely to cost significantly more in grid environments. In short, the distributed processing community needs accurate, succinct and complete measurements of collective communications performance. Since successive collective communications can often proceed concurrently, accurately measuring them is difficult. Some benchmarks use knowledge of the communication algorithm to predict the
Computational approaches to computational aero-acoustics
NASA Technical Reports Server (NTRS)
Hardin, Jay C.
1996-01-01
The various techniques by which the goal of computational aeroacoustics (the calculation and noise prediction of a fluctuating fluid flow) may be achieved are reviewed. The governing equations for compressible fluid flow are presented. The direct numerical simulation approach is shown to be computationally intensive for high Reynolds number viscous flows. Therefore, other approaches, such as the acoustic analogy, vortex models and various perturbation techniques that aim to break the analysis into a viscous part and an acoustic part are presented. The choice of the approach is shown to be problem dependent.
Computational approaches to vision
NASA Technical Reports Server (NTRS)
Barrow, H. G.; Tenenbaum, J. M.
1986-01-01
Vision is examined in terms of a computational process, and the competence, structure, and control of computer vision systems are analyzed. Theoretical and experimental data on the formation of a computer vision system are discussed. Consideration is given to early vision, the recovery of intrinsic surface characteristics, higher levels of interpretation, and system integration and control. A computational visual processing model is proposed and its architecture and operation are described. Examples of state-of-the-art vision systems, which include some of the levels of representation and processing mechanisms, are presented.
Kearns, F L; Hudson, P S; Boresch, S; Woodcock, H L
2016-01-01
Enzyme activity is inherently linked to free energies of transition states, ligand binding, protonation/deprotonation, etc.; these free energies, and thus enzyme function, can be affected by residue mutations, allosterically induced conformational changes, and much more. Therefore, being able to predict free energies associated with enzymatic processes is critical to understanding and predicting their function. Free energy simulation (FES) has historically been a computational challenge as it requires both the accurate description of inter- and intramolecular interactions and adequate sampling of all relevant conformational degrees of freedom. The hybrid quantum mechanical molecular mechanical (QM/MM) framework is the current tool of choice when accurate computations of macromolecular systems are essential. Unfortunately, robust and efficient approaches that employ the high levels of computational theory needed to accurately describe many reactive processes (ie, ab initio, DFT), while also including explicit solvation effects and accounting for extensive conformational sampling are essentially nonexistent. In this chapter, we will give a brief overview of two recently developed methods that mitigate several major challenges associated with QM/MM FES: the QM non-Boltzmann Bennett's acceptance ratio method and the QM nonequilibrium work method. We will also describe usage of these methods to calculate free energies associated with (1) relative properties and (2) along reaction paths, using simple test cases with relevance to enzymes examples.
Kearns, F L; Hudson, P S; Boresch, S; Woodcock, H L
2016-01-01
Enzyme activity is inherently linked to free energies of transition states, ligand binding, protonation/deprotonation, etc.; these free energies, and thus enzyme function, can be affected by residue mutations, allosterically induced conformational changes, and much more. Therefore, being able to predict free energies associated with enzymatic processes is critical to understanding and predicting their function. Free energy simulation (FES) has historically been a computational challenge as it requires both the accurate description of inter- and intramolecular interactions and adequate sampling of all relevant conformational degrees of freedom. The hybrid quantum mechanical molecular mechanical (QM/MM) framework is the current tool of choice when accurate computations of macromolecular systems are essential. Unfortunately, robust and efficient approaches that employ the high levels of computational theory needed to accurately describe many reactive processes (ie, ab initio, DFT), while also including explicit solvation effects and accounting for extensive conformational sampling are essentially nonexistent. In this chapter, we will give a brief overview of two recently developed methods that mitigate several major challenges associated with QM/MM FES: the QM non-Boltzmann Bennett's acceptance ratio method and the QM nonequilibrium work method. We will also describe usage of these methods to calculate free energies associated with (1) relative properties and (2) along reaction paths, using simple test cases with relevance to enzymes examples. PMID:27498635
Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Peña, Isabel; Cabezas, Carlos; Alonso, José L.
2015-01-01
The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier Transform Microwave spectrometers. The joint experimental – computational study allowed us to determine accurate molecular structure and spectroscopic properties for the title molecule, but more important, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules. PMID:24002739
NASA Astrophysics Data System (ADS)
Zhao, Xiao-mei; Xie, Dong-fan; Li, Qi
2015-02-01
With the development of intelligent transport system, advanced information feedback strategies have been developed to reduce traffic congestion and enhance the capacity. However, previous strategies provide accurate information to travelers and our simulation results show that accurate information brings negative effects, especially in delay case. Because travelers prefer to the best condition route with accurate information, and delayed information cannot reflect current traffic condition but past. Then travelers make wrong routing decisions, causing the decrease of the capacity and the increase of oscillations and the system deviating from the equilibrium. To avoid the negative effect, bounded rationality is taken into account by introducing a boundedly rational threshold BR. When difference between two routes is less than the BR, routes have equal probability to be chosen. The bounded rationality is helpful to improve the efficiency in terms of capacity, oscillation and the gap deviating from the system equilibrium.
An Accurate and Computationally Efficient Model for Membrane-Type Circular-Symmetric Micro-Hotplates
Khan, Usman; Falconi, Christian
2014-01-01
Ideally, the design of high-performance micro-hotplates would require a large number of simulations because of the existence of many important design parameters as well as the possibly crucial effects of both spread and drift. However, the computational cost of FEM simulations, which are the only available tool for accurately predicting the temperature in micro-hotplates, is very high. As a result, micro-hotplate designers generally have no effective simulation-tools for the optimization. In order to circumvent these issues, here, we propose a model for practical circular-symmetric micro-hot-plates which takes advantage of modified Bessel functions, computationally efficient matrix-approach for considering the relevant boundary conditions, Taylor linearization for modeling the Joule heating and radiation losses, and external-region-segmentation strategy in order to accurately take into account radiation losses in the entire micro-hotplate. The proposed model is almost as accurate as FEM simulations and two to three orders of magnitude more computationally efficient (e.g., 45 s versus more than 8 h). The residual errors, which are mainly associated to the undesired heating in the electrical contacts, are small (e.g., few degrees Celsius for an 800 °C operating temperature) and, for important analyses, almost constant. Therefore, we also introduce a computationally-easy single-FEM-compensation strategy in order to reduce the residual errors to about 1 °C. As illustrative examples of the power of our approach, we report the systematic investigation of a spread in the membrane thermal conductivity and of combined variations of both ambient and bulk temperatures. Our model enables a much faster characterization of micro-hotplates and, thus, a much more effective optimization prior to fabrication. PMID:24763214
A new approach to constructing efficient stiffly accurate EPIRK methods
NASA Astrophysics Data System (ADS)
Rainwater, G.; Tokman, M.
2016-10-01
The structural flexibility of the exponential propagation iterative methods of Runge-Kutta type (EPIRK) enables construction of particularly efficient exponential time integrators. While the EPIRK methods have been shown to perform well on stiff problems, all of the schemes proposed up to now have been derived using classical order conditions. In this paper we extend the stiff order conditions and the convergence theory developed for the exponential Rosenbrock methods to the EPIRK integrators. We derive stiff order conditions for the EPIRK methods and develop algorithms to solve them to obtain specific schemes. Moreover, we propose a new approach to constructing particularly efficient EPIRK integrators that are optimized to work with an adaptive Krylov algorithm. We use a set of numerical examples to illustrate the computational advantages that the newly constructed EPIRK methods offer compared to previously proposed exponential integrators.
Approaches for the accurate definition of geological time boundaries
NASA Astrophysics Data System (ADS)
Schaltegger, Urs; Baresel, Björn; Ovtcharova, Maria; Goudemand, Nicolas; Bucher, Hugo
2015-04-01
Which strategies lead to the most precise and accurate date of a given geological boundary? Geological units are usually defined by the occurrence of characteristic taxa and hence boundaries between these geological units correspond to dramatic faunal and/or floral turnovers and they are primarily defined using first or last occurrences of index species, or ideally by the separation interval between two consecutive, characteristic associations of fossil taxa. These boundaries need to be defined in a way that enables their worldwide recognition and correlation across different stratigraphic successions, using tools as different as bio-, magneto-, and chemo-stratigraphy, and astrochronology. Sedimentary sequences can be dated in numerical terms by applying high-precision chemical-abrasion, isotope-dilution, thermal-ionization mass spectrometry (CA-ID-TIMS) U-Pb age determination to zircon (ZrSiO4) in intercalated volcanic ashes. But, though volcanic activity is common in geological history, ashes are not necessarily close to the boundary we would like to date precisely and accurately. In addition, U-Pb zircon data sets may be very complex and difficult to interpret in terms of the age of ash deposition. To overcome these difficulties we use a multi-proxy approach we applied to the precise and accurate dating of the Permo-Triassic and Early-Middle Triassic boundaries in South China. a) Dense sampling of ashes across the critical time interval and a sufficiently large number of analysed zircons per ash sample can guarantee the recognition of all system complexities. Geochronological datasets from U-Pb dating of volcanic zircon may indeed combine effects of i) post-crystallization Pb loss from percolation of hydrothermal fluids (even using chemical abrasion), with ii) age dispersion from prolonged residence of earlier crystallized zircon in the magmatic system. As a result, U-Pb dates of individual zircons are both apparently younger and older than the depositional age
A Machine Learning Approach for Accurate Annotation of Noncoding RNAs.
Song, Yinglei; Liu, Chunmei; Wang, Zhi
2015-01-01
Searching genomes to locate noncoding RNA genes with known secondary structure is an important problem in bioinformatics. In general, the secondary structure of a searched noncoding RNA is defined with a structure model constructed from the structural alignment of a set of sequences from its family. Computing the optimal alignment between a sequence and a structure model is the core part of an algorithm that can search genomes for noncoding RNAs. In practice, a single structure model may not be sufficient to capture all crucial features important for a noncoding RNA family. In this paper, we develop a novel machine learning approach that can efficiently search genomes for noncoding RNAs with high accuracy. During the search procedure, a sequence segment in the searched genome sequence is processed and a feature vector is extracted to represent it. Based on the feature vector, a classifier is used to determine whether the sequence segment is the searched ncRNA or not. Our testing results show that this approach is able to efficiently capture crucial features of a noncoding RNA family. Compared with existing search tools, it significantly improves the accuracy of genome annotation. PMID:26357266
A Machine Learning Approach for Accurate Annotation of Noncoding RNAs
Liu, Chunmei; Wang, Zhi
2016-01-01
Searching genomes to locate noncoding RNA genes with known secondary structure is an important problem in bioinformatics. In general, the secondary structure of a searched noncoding RNA is defined with a structure model constructed from the structural alignment of a set of sequences from its family. Computing the optimal alignment between a sequence and a structure model is the core part of an algorithm that can search genomes for noncoding RNAs. In practice, a single structure model may not be sufficient to capture all crucial features important for a noncoding RNA family. In this paper, we develop a novel machine learning approach that can efficiently search genomes for noncoding RNAs with high accuracy. During the search procedure, a sequence segment in the searched genome sequence is processed and a feature vector is extracted to represent it. Based on the feature vector, a classifier is used to determine whether the sequence segment is the searched ncRNA or not. Our testing results show that this approach is able to efficiently capture crucial features of a noncoding RNA family. Compared with existing search tools, it significantly improves the accuracy of genome annotation. PMID:26357266
Active contour approach for accurate quantitative airway analysis
NASA Astrophysics Data System (ADS)
Odry, Benjamin L.; Kiraly, Atilla P.; Slabaugh, Greg G.; Novak, Carol L.; Naidich, David P.; Lerallut, Jean-Francois
2008-03-01
Chronic airway disease causes structural changes in the lungs including peribronchial thickening and airway dilatation. Multi-detector computed tomography (CT) yields detailed near-isotropic images of the lungs, and thus the potential to obtain quantitative measurements of lumen diameter and airway wall thickness. Such measurements would allow standardized assessment, and physicians to diagnose and locate airway abnormalities, adapt treatment, and monitor progress over time. However, due to the sheer number of airways per patient, systematic analysis is infeasible in routine clinical practice without automation. We have developed an automated and real-time method based on active contours to estimate both airway lumen and wall dimensions; the method does not require manual contour initialization but only a starting point on the targeted airway. While the lumen contour segmentation is purely region-based, the estimation of the outer diameter considers the inner wall segmentation as well as local intensity variation, in order anticipate the presence of nearby arteries and exclude them. These properties make the method more robust than the Full-Width Half Maximum (FWHM) approach. Results are demonstrated on a phantom dataset with known dimensions and on a human dataset where the automated measurements are compared against two human operators. The average error on the phantom measurements was 0.10mm and 0.14mm for inner and outer diameters, showing sub-voxel accuracy. Similarly, the mean variation from the average manual measurement was 0.14mm and 0.18mm for inner and outer diameters respectively.
Loewe, Axel; Wilhelms, Mathias; Schmid, Jochen; Krause, Mathias J.; Fischer, Fathima; Thomas, Dierk; Scholz, Eberhard P.; Dössel, Olaf; Seemann, Gunnar
2016-01-01
Computational models of cardiac electrophysiology provided insights into arrhythmogenesis and paved the way toward tailored therapies in the last years. To fully leverage in silico models in future research, these models need to be adapted to reflect pathologies, genetic alterations, or pharmacological effects, however. A common approach is to leave the structure of established models unaltered and estimate the values of a set of parameters. Today’s high-throughput patch clamp data acquisition methods require robust, unsupervised algorithms that estimate parameters both accurately and reliably. In this work, two classes of optimization approaches are evaluated: gradient-based trust-region-reflective and derivative-free particle swarm algorithms. Using synthetic input data and different ion current formulations from the Courtemanche et al. electrophysiological model of human atrial myocytes, we show that neither of the two schemes alone succeeds to meet all requirements. Sequential combination of the two algorithms did improve the performance to some extent but not satisfactorily. Thus, we propose a novel hybrid approach coupling the two algorithms in each iteration. This hybrid approach yielded very accurate estimates with minimal dependency on the initial guess using synthetic input data for which a ground truth parameter set exists. When applied to measured data, the hybrid approach yielded the best fit, again with minimal variation. Using the proposed algorithm, a single run is sufficient to estimate the parameters. The degree of superiority over the other investigated algorithms in terms of accuracy and robustness depended on the type of current. In contrast to the non-hybrid approaches, the proposed method proved to be optimal for data of arbitrary signal to noise ratio. The hybrid algorithm proposed in this work provides an important tool to integrate experimental data into computational models both accurately and robustly allowing to assess the often non
An approach for the accurate measurement of social morality levels.
Liu, Haiyan; Chen, Xia; Zhang, Bo
2013-01-01
In the social sciences, computer-based modeling has become an increasingly important tool receiving widespread attention. However, the derivation of the quantitative relationships linking individual moral behavior and social morality levels, so as to provide a useful basis for social policy-making, remains a challenge in the scholarly literature today. A quantitative measurement of morality from the perspective of complexity science constitutes an innovative attempt. Based on the NetLogo platform, this article examines the effect of various factors on social morality levels, using agents modeling moral behavior, immoral behavior, and a range of environmental social resources. Threshold values for the various parameters are obtained through sensitivity analysis; and practical solutions are proposed for reversing declines in social morality levels. The results show that: (1) Population size may accelerate or impede the speed with which immoral behavior comes to determine the overall level of social morality, but it has no effect on the level of social morality itself; (2) The impact of rewards and punishment on social morality levels follows the "5∶1 rewards-to-punishment rule," which is to say that 5 units of rewards have the same effect as 1 unit of punishment; (3) The abundance of public resources is inversely related to the level of social morality; (4) When the cost of population mobility reaches 10% of the total energy level, immoral behavior begins to be suppressed (i.e. the 1/10 moral cost rule). The research approach and methods presented in this paper successfully address the difficulties involved in measuring social morality levels, and promise extensive application potentials.
An Approach for the Accurate Measurement of Social Morality Levels
Liu, Haiyan; Chen, Xia; Zhang, Bo
2013-01-01
In the social sciences, computer-based modeling has become an increasingly important tool receiving widespread attention. However, the derivation of the quantitative relationships linking individual moral behavior and social morality levels, so as to provide a useful basis for social policy-making, remains a challenge in the scholarly literature today. A quantitative measurement of morality from the perspective of complexity science constitutes an innovative attempt. Based on the NetLogo platform, this article examines the effect of various factors on social morality levels, using agents modeling moral behavior, immoral behavior, and a range of environmental social resources. Threshold values for the various parameters are obtained through sensitivity analysis; and practical solutions are proposed for reversing declines in social morality levels. The results show that: (1) Population size may accelerate or impede the speed with which immoral behavior comes to determine the overall level of social morality, but it has no effect on the level of social morality itself; (2) The impact of rewards and punishment on social morality levels follows the “5∶1 rewards-to-punishment rule,” which is to say that 5 units of rewards have the same effect as 1 unit of punishment; (3) The abundance of public resources is inversely related to the level of social morality; (4) When the cost of population mobility reaches 10% of the total energy level, immoral behavior begins to be suppressed (i.e. the 1/10 moral cost rule). The research approach and methods presented in this paper successfully address the difficulties involved in measuring social morality levels, and promise extensive application potentials. PMID:24312189
Groundtruth approach to accurate quantitation of fluorescence microarrays
Mascio-Kegelmeyer, L; Tomascik-Cheeseman, L; Burnett, M S; van Hummelen, P; Wyrobek, A J
2000-12-01
To more accurately measure fluorescent signals from microarrays, we calibrated our acquisition and analysis systems by using groundtruth samples comprised of known quantities of red and green gene-specific DNA probes hybridized to cDNA targets. We imaged the slides with a full-field, white light CCD imager and analyzed them with our custom analysis software. Here we compare, for multiple genes, results obtained with and without preprocessing (alignment, color crosstalk compensation, dark field subtraction, and integration time). We also evaluate the accuracy of various image processing and analysis techniques (background subtraction, segmentation, quantitation and normalization). This methodology calibrates and validates our system for accurate quantitative measurement of microarrays. Specifically, we show that preprocessing the images produces results significantly closer to the known ground-truth for these samples.
CoMOGrad and PHOG: From Computer Vision to Fast and Accurate Protein Tertiary Structure Retrieval
Karim, Rezaul; Aziz, Mohd. Momin Al; Shatabda, Swakkhar; Rahman, M. Sohel; Mia, Md. Abul Kashem; Zaman, Farhana; Rakin, Salman
2015-01-01
The number of entries in a structural database of proteins is increasing day by day. Methods for retrieving protein tertiary structures from such a large database have turn out to be the key to comparative analysis of structures that plays an important role to understand proteins and their functions. In this paper, we present fast and accurate methods for the retrieval of proteins having tertiary structures similar to a query protein from a large database. Our proposed methods borrow ideas from the field of computer vision. The speed and accuracy of our methods come from the two newly introduced features- the co-occurrence matrix of the oriented gradient and pyramid histogram of oriented gradient- and the use of Euclidean distance as the distance measure. Experimental results clearly indicate the superiority of our approach in both running time and accuracy. Our method is readily available for use from this website: http://research.buet.ac.bd:8080/Comograd/. PMID:26293226
PERTURBATION APPROACH FOR QUANTUM COMPUTATION
G. P. BERMAN; D. I. KAMENEV; V. I. TSIFRINOVICH
2001-04-01
We discuss how to simulate errors in the implementation of simple quantum logic operations in a nuclear spin quantum computer with many qubits, using radio-frequency pulses. We verify our perturbation approach using the exact solutions for relatively small (L = 10) number of qubits.
Development of highly accurate approximate scheme for computing the charge transfer integral.
Pershin, Anton; Szalay, Péter G
2015-08-21
The charge transfer integral is a key parameter required by various theoretical models to describe charge transport properties, e.g., in organic semiconductors. The accuracy of this important property depends on several factors, which include the level of electronic structure theory and internal simplifications of the applied formalism. The goal of this paper is to identify the performance of various approximate approaches of the latter category, while using the high level equation-of-motion coupled cluster theory for the electronic structure. The calculations have been performed on the ethylene dimer as one of the simplest model systems. By studying different spatial perturbations, it was shown that while both energy split in dimer and fragment charge difference methods are equivalent with the exact formulation for symmetrical displacements, they are less efficient when describing transfer integral along the asymmetric alteration coordinate. Since the "exact" scheme was found computationally expensive, we examine the possibility to obtain the asymmetric fluctuation of the transfer integral by a Taylor expansion along the coordinate space. By exploring the efficiency of this novel approach, we show that the Taylor expansion scheme represents an attractive alternative to the "exact" calculations due to a substantial reduction of computational costs, when a considerably large region of the potential energy surface is of interest. Moreover, we show that the Taylor expansion scheme, irrespective of the dimer symmetry, is very accurate for the entire range of geometry fluctuations that cover the space the molecule accesses at room temperature. PMID:26298117
Development of highly accurate approximate scheme for computing the charge transfer integral
Pershin, Anton; Szalay, Péter G.
2015-08-21
The charge transfer integral is a key parameter required by various theoretical models to describe charge transport properties, e.g., in organic semiconductors. The accuracy of this important property depends on several factors, which include the level of electronic structure theory and internal simplifications of the applied formalism. The goal of this paper is to identify the performance of various approximate approaches of the latter category, while using the high level equation-of-motion coupled cluster theory for the electronic structure. The calculations have been performed on the ethylene dimer as one of the simplest model systems. By studying different spatial perturbations, it was shown that while both energy split in dimer and fragment charge difference methods are equivalent with the exact formulation for symmetrical displacements, they are less efficient when describing transfer integral along the asymmetric alteration coordinate. Since the “exact” scheme was found computationally expensive, we examine the possibility to obtain the asymmetric fluctuation of the transfer integral by a Taylor expansion along the coordinate space. By exploring the efficiency of this novel approach, we show that the Taylor expansion scheme represents an attractive alternative to the “exact” calculations due to a substantial reduction of computational costs, when a considerably large region of the potential energy surface is of interest. Moreover, we show that the Taylor expansion scheme, irrespective of the dimer symmetry, is very accurate for the entire range of geometry fluctuations that cover the space the molecule accesses at room temperature.
NASA Technical Reports Server (NTRS)
Liu, Yen; Vinokur, Marcel
1989-01-01
This paper treats the accurate and efficient calculation of thermodynamic properties of arbitrary gas mixtures for equilibrium flow computations. New improvements in the Stupochenko-Jaffe model for the calculation of thermodynamic properties of diatomic molecules are presented. A unified formulation of equilibrium calculations for gas mixtures in terms of irreversible entropy is given. Using a highly accurate thermo-chemical data base, a new, efficient and vectorizable search algorithm is used to construct piecewise interpolation procedures with generate accurate thermodynamic variable and their derivatives required by modern computational algorithms. Results are presented for equilibrium air, and compared with those given by the Srinivasan program.
Candel, A.; Kabel, A.; Lee, L.; Li, Z.; Limborg, C.; Ng, C.; Prudencio, E.; Schussman, G.; Uplenchwar, R.; Ko, K.; /SLAC
2009-06-19
Over the past years, SLAC's Advanced Computations Department (ACD), under SciDAC sponsorship, has developed a suite of 3D (2D) parallel higher-order finite element (FE) codes, T3P (T2P) and Pic3P (Pic2P), aimed at accurate, large-scale simulation of wakefields and particle-field interactions in radio-frequency (RF) cavities of complex shape. The codes are built on the FE infrastructure that supports SLAC's frequency domain codes, Omega3P and S3P, to utilize conformal tetrahedral (triangular)meshes, higher-order basis functions and quadratic geometry approximation. For time integration, they adopt an unconditionally stable implicit scheme. Pic3P (Pic2P) extends T3P (T2P) to treat charged-particle dynamics self-consistently using the PIC (particle-in-cell) approach, the first such implementation on a conformal, unstructured grid using Whitney basis functions. Examples from applications to the International Linear Collider (ILC), Positron Electron Project-II (PEP-II), Linac Coherent Light Source (LCLS) and other accelerators will be presented to compare the accuracy and computational efficiency of these codes versus their counterparts using structured grids.
Haley, William E; Ibrahim, El-Sayed H; Qu, Mingliang; Cernigliaro, Joseph G; Goldfarb, David S; McCollough, Cynthia H
2015-01-01
Dual-energy computed tomography (DECT) has recently been suggested as the imaging modality of choice for kidney stones due to its ability to provide information on stone composition. Standard postprocessing of the dual-energy images accurately identifies uric acid stones, but not other types. Cystine stones can be identified from DECT images when analyzed with advanced postprocessing. This case report describes clinical implications of accurate diagnosis of cystine stones using DECT.
Creation of Anatomically Accurate Computer-Aided Design (CAD) Solid Models from Medical Images
NASA Technical Reports Server (NTRS)
Stewart, John E.; Graham, R. Scott; Samareh, Jamshid A.; Oberlander, Eric J.; Broaddus, William C.
1999-01-01
Most surgical instrumentation and implants used in the world today are designed with sophisticated Computer-Aided Design (CAD)/Computer-Aided Manufacturing (CAM) software. This software automates the mechanical development of a product from its conceptual design through manufacturing. CAD software also provides a means of manipulating solid models prior to Finite Element Modeling (FEM). Few surgical products are designed in conjunction with accurate CAD models of human anatomy because of the difficulty with which these models are created. We have developed a novel technique that creates anatomically accurate, patient specific CAD solids from medical images in a matter of minutes.
Kouznetsov, Alexei; Tambasco, Mauro
2011-03-15
Purpose: To develop and validate a fast and accurate method that uses computed tomography (CT) voxel data to estimate absorbed radiation dose at a point of interest (POI) or series of POIs from a kilovoltage (kV) imaging procedure. Methods: The authors developed an approach that computes absorbed radiation dose at a POI by numerically evaluating the linear Boltzmann transport equation (LBTE) using a combination of deterministic and Monte Carlo (MC) techniques. This hybrid approach accounts for material heterogeneity with a level of accuracy comparable to the general MC algorithms. Also, the dose at a POI is computed within seconds using the Intel Core i7 CPU 920 2.67 GHz quad core architecture, and the calculations are performed using CT voxel data, making it flexible and feasible for clinical applications. To validate the method, the authors constructed and acquired a CT scan of a heterogeneous block phantom consisting of a succession of slab densities: Tissue (1.29 cm), bone (2.42 cm), lung (4.84 cm), bone (1.37 cm), and tissue (4.84 cm). Using the hybrid transport method, the authors computed the absorbed doses at a set of points along the central axis and x direction of the phantom for an isotropic 125 kVp photon spectral point source located along the central axis 92.7 cm above the phantom surface. The accuracy of the results was compared to those computed with MCNP, which was cross-validated with EGSnrc, and served as the benchmark for validation. Results: The error in the depth dose ranged from -1.45% to +1.39% with a mean and standard deviation of -0.12% and 0.66%, respectively. The error in the x profile ranged from -1.3% to +0.9%, with standard deviations of -0.3% and 0.5%, respectively. The number of photons required to achieve these results was 1x10{sup 6}. Conclusions: The voxel-based hybrid method evaluates the LBTE rapidly and accurately to estimate the absorbed x-ray dose at any POI or series of POIs from a kV imaging procedure.
Computer Series, 101: Accurate Equations of State in Computational Chemistry Projects.
ERIC Educational Resources Information Center
Albee, David; Jones, Edward
1989-01-01
Discusses the use of computers in chemistry courses at the United States Military Academy. Provides two examples of computer projects: (1) equations of state, and (2) solving for molar volume. Presents BASIC and PASCAL listings for the second project. Lists 10 applications for physical chemistry. (MVL)
Aeroacoustic Flow Phenomena Accurately Captured by New Computational Fluid Dynamics Method
NASA Technical Reports Server (NTRS)
Blech, Richard A.
2002-01-01
One of the challenges in the computational fluid dynamics area is the accurate calculation of aeroacoustic phenomena, especially in the presence of shock waves. One such phenomenon is "transonic resonance," where an unsteady shock wave at the throat of a convergent-divergent nozzle results in the emission of acoustic tones. The space-time Conservation-Element and Solution-Element (CE/SE) method developed at the NASA Glenn Research Center can faithfully capture the shock waves, their unsteady motion, and the generated acoustic tones. The CE/SE method is a revolutionary new approach to the numerical modeling of physical phenomena where features with steep gradients (e.g., shock waves, phase transition, etc.) must coexist with those having weaker variations. The CE/SE method does not require the complex interpolation procedures (that allow for the possibility of a shock between grid cells) used by many other methods to transfer information between grid cells. These interpolation procedures can add too much numerical dissipation to the solution process. Thus, while shocks are resolved, weaker waves, such as acoustic waves, are washed out.
Computational Approaches to Vestibular Research
NASA Technical Reports Server (NTRS)
Ross, Muriel D.; Wade, Charles E. (Technical Monitor)
1994-01-01
The Biocomputation Center at NASA Ames Research Center is dedicated to a union between computational, experimental and theoretical approaches to the study of neuroscience and of life sciences in general. The current emphasis is on computer reconstruction and visualization of vestibular macular architecture in three-dimensions (3-D), and on mathematical modeling and computer simulation of neural activity in the functioning system. Our methods are being used to interpret the influence of spaceflight on mammalian vestibular maculas in a model system, that of the adult Sprague-Dawley rat. More than twenty 3-D reconstructions of type I and type II hair cells and their afferents have been completed by digitization of contours traced from serial sections photographed in a transmission electron microscope. This labor-intensive method has now been replace d by a semiautomated method developed in the Biocomputation Center in which conventional photography is eliminated. All viewing, storage and manipulation of original data is done using Silicon Graphics workstations. Recent improvements to the software include a new mesh generation method for connecting contours. This method will permit the investigator to describe any surface, regardless of complexity, including highly branched structures such as are routinely found in neurons. This same mesh can be used for 3-D, finite volume simulation of synapse activation and voltage spread on neuronal surfaces visualized via the reconstruction process. These simulations help the investigator interpret the relationship between neuroarchitecture and physiology, and are of assistance in determining which experiments will best test theoretical interpretations. Data are also used to develop abstract, 3-D models that dynamically display neuronal activity ongoing in the system. Finally, the same data can be used to visualize the neural tissue in a virtual environment. Our exhibit will depict capabilities of our computational approaches and
[A historical approach to computing].
Babini, N
1996-12-01
Half a century after computers' conception, its effects, already reaching all human domains, seem to aim at becoming a universal transition similar to that one which marked in Occident the passage from artisanal production to industrial production among the 18 and 19 centuries, as from mechanisation to universal automation. It's considered that if this supposition may be correct, it would be urgent to intensify the historical approach of Informatics already present in may countries but not in ours. It's proposed the gradual incorporation of history of informatics in university careers beginning from research centers including teachers and researchers preparation, production and publication of works and the creation of museums and archives, to preserve physical testimonies and origin documents and the initial evolution of this scientific-technical invention which honours our century.
Computer-based personality judgments are more accurate than those made by humans
Youyou, Wu; Kosinski, Michal; Stillwell, David
2015-01-01
Judging others’ personalities is an essential skill in successful social living, as personality is a key driver behind people’s interactions, behaviors, and emotions. Although accurate personality judgments stem from social-cognitive skills, developments in machine learning show that computer models can also make valid judgments. This study compares the accuracy of human and computer-based personality judgments, using a sample of 86,220 volunteers who completed a 100-item personality questionnaire. We show that (i) computer predictions based on a generic digital footprint (Facebook Likes) are more accurate (r = 0.56) than those made by the participants’ Facebook friends using a personality questionnaire (r = 0.49); (ii) computer models show higher interjudge agreement; and (iii) computer personality judgments have higher external validity when predicting life outcomes such as substance use, political attitudes, and physical health; for some outcomes, they even outperform the self-rated personality scores. Computers outpacing humans in personality judgment presents significant opportunities and challenges in the areas of psychological assessment, marketing, and privacy. PMID:25583507
Computer-based personality judgments are more accurate than those made by humans.
Youyou, Wu; Kosinski, Michal; Stillwell, David
2015-01-27
Judging others' personalities is an essential skill in successful social living, as personality is a key driver behind people's interactions, behaviors, and emotions. Although accurate personality judgments stem from social-cognitive skills, developments in machine learning show that computer models can also make valid judgments. This study compares the accuracy of human and computer-based personality judgments, using a sample of 86,220 volunteers who completed a 100-item personality questionnaire. We show that (i) computer predictions based on a generic digital footprint (Facebook Likes) are more accurate (r = 0.56) than those made by the participants' Facebook friends using a personality questionnaire (r = 0.49); (ii) computer models show higher interjudge agreement; and (iii) computer personality judgments have higher external validity when predicting life outcomes such as substance use, political attitudes, and physical health; for some outcomes, they even outperform the self-rated personality scores. Computers outpacing humans in personality judgment presents significant opportunities and challenges in the areas of psychological assessment, marketing, and privacy.
Computer-based personality judgments are more accurate than those made by humans.
Youyou, Wu; Kosinski, Michal; Stillwell, David
2015-01-27
Judging others' personalities is an essential skill in successful social living, as personality is a key driver behind people's interactions, behaviors, and emotions. Although accurate personality judgments stem from social-cognitive skills, developments in machine learning show that computer models can also make valid judgments. This study compares the accuracy of human and computer-based personality judgments, using a sample of 86,220 volunteers who completed a 100-item personality questionnaire. We show that (i) computer predictions based on a generic digital footprint (Facebook Likes) are more accurate (r = 0.56) than those made by the participants' Facebook friends using a personality questionnaire (r = 0.49); (ii) computer models show higher interjudge agreement; and (iii) computer personality judgments have higher external validity when predicting life outcomes such as substance use, political attitudes, and physical health; for some outcomes, they even outperform the self-rated personality scores. Computers outpacing humans in personality judgment presents significant opportunities and challenges in the areas of psychological assessment, marketing, and privacy. PMID:25583507
Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach.
Saa, Pedro A; Nielsen, Lars K
2016-01-01
Kinetic models are essential to quantitatively understand and predict the behaviour of metabolic networks. Detailed and thermodynamically feasible kinetic models of metabolism are inherently difficult to formulate and fit. They have a large number of heterogeneous parameters, are non-linear and have complex interactions. Many powerful fitting strategies are ruled out by the intractability of the likelihood function. Here, we have developed a computational framework capable of fitting feasible and accurate kinetic models using Approximate Bayesian Computation. This framework readily supports advanced modelling features such as model selection and model-based experimental design. We illustrate this approach on the tightly-regulated mammalian methionine cycle. Sampling from the posterior distribution, the proposed framework generated thermodynamically feasible parameter samples that converged on the true values, and displayed remarkable prediction accuracy in several validation tests. Furthermore, a posteriori analysis of the parameter distributions enabled appraisal of the systems properties of the network (e.g., control structure) and key metabolic regulations. Finally, the framework was used to predict missing allosteric interactions. PMID:27417285
Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach
Saa, Pedro A.; Nielsen, Lars K.
2016-01-01
Kinetic models are essential to quantitatively understand and predict the behaviour of metabolic networks. Detailed and thermodynamically feasible kinetic models of metabolism are inherently difficult to formulate and fit. They have a large number of heterogeneous parameters, are non-linear and have complex interactions. Many powerful fitting strategies are ruled out by the intractability of the likelihood function. Here, we have developed a computational framework capable of fitting feasible and accurate kinetic models using Approximate Bayesian Computation. This framework readily supports advanced modelling features such as model selection and model-based experimental design. We illustrate this approach on the tightly-regulated mammalian methionine cycle. Sampling from the posterior distribution, the proposed framework generated thermodynamically feasible parameter samples that converged on the true values, and displayed remarkable prediction accuracy in several validation tests. Furthermore, a posteriori analysis of the parameter distributions enabled appraisal of the systems properties of the network (e.g., control structure) and key metabolic regulations. Finally, the framework was used to predict missing allosteric interactions. PMID:27417285
Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Peña, Isabel; Cabezas, Carlos; Alonso, José L
2013-10-21
The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier transform microwave spectrometers. The joint experimental-computational study allowed us to determine the accurate molecular structure and spectroscopic properties of the title molecule, but more importantly, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules.
A Unified Methodology for Computing Accurate Quaternion Color Moments and Moment Invariants.
Karakasis, Evangelos G; Papakostas, George A; Koulouriotis, Dimitrios E; Tourassis, Vassilios D
2014-02-01
In this paper, a general framework for computing accurate quaternion color moments and their corresponding invariants is proposed. The proposed unified scheme arose by studying the characteristics of different orthogonal polynomials. These polynomials are used as kernels in order to form moments, the invariants of which can easily be derived. The resulted scheme permits the usage of any polynomial-like kernel in a unified and consistent way. The resulted moments and moment invariants demonstrate robustness to noisy conditions and high discriminative power. Additionally, in the case of continuous moments, accurate computations take place to avoid approximation errors. Based on this general methodology, the quaternion Tchebichef, Krawtchouk, Dual Hahn, Legendre, orthogonal Fourier-Mellin, pseudo Zernike and Zernike color moments, and their corresponding invariants are introduced. A selected paradigm presents the reconstruction capability of each moment family, whereas proper classification scenarios evaluate the performance of color moment invariants. PMID:24216719
NASA Astrophysics Data System (ADS)
Frolov, Alexei M.; Wardlaw, David M.
2016-09-01
We discuss an approach to accurate numerical computations of slowly convergent properties in two-electron atoms/ions which include the negatively charged Ps- ( e - e + e -) and H- ions, He atom and positively charged, helium-like ions from Li+ to Ni26+. All these ions are considered in their ground 11S-state(s). The slowly convergent properties selected in this study include the electron-nulceus ( r 2k eN) and electron-electron ( r 2k ee) expectation values for k = 2, 3, 4 and 5.
NASA Astrophysics Data System (ADS)
Zhang, Shunli; Zhang, Dinghua; Gong, Hao; Ghasemalizadeh, Omid; Wang, Ge; Cao, Guohua
2014-11-01
Iterative algorithms, such as the algebraic reconstruction technique (ART), are popular for image reconstruction. For iterative reconstruction, the area integral model (AIM) is more accurate for better reconstruction quality than the line integral model (LIM). However, the computation of the system matrix for AIM is more complex and time-consuming than that for LIM. Here, we propose a fast and accurate method to compute the system matrix for AIM. First, we calculate the intersection of each boundary line of a narrow fan-beam with pixels in a recursive and efficient manner. Then, by grouping the beam-pixel intersection area into six types according to the slopes of the two boundary lines, we analytically compute the intersection area of the narrow fan-beam with the pixels in a simple algebraic fashion. Overall, experimental results show that our method is about three times faster than the Siddon algorithm and about two times faster than the distance-driven model (DDM) in computation of the system matrix. The reconstruction speed of our AIM-based ART is also faster than the LIM-based ART that uses the Siddon algorithm and DDM-based ART, for one iteration. The fast reconstruction speed of our method was accomplished without compromising the image quality.
Yoshidome, Takashi; Ekimoto, Toru; Matubayasi, Nobuyuki; Harano, Yuichi; Kinoshita, Masahiro; Ikeguchi, Mitsunori
2015-05-01
The hydration free energy (HFE) is a crucially important physical quantity to discuss various chemical processes in aqueous solutions. Although an explicit-solvent computation with molecular dynamics (MD) simulations is a preferable treatment of the HFE, huge computational load has been inevitable for large, complex solutes like proteins. In the present paper, we propose an efficient computation method for the HFE. In our method, the HFE is computed as a sum of 〈UUV〉/2 (〈UUV〉 is the ensemble average of the sum of pair interaction energy between solute and water molecule) and the water reorganization term mainly reflecting the excluded volume effect. Since 〈UUV〉 can readily be computed through a MD of the system composed of solute and water, an efficient computation of the latter term leads to a reduction of computational load. We demonstrate that the water reorganization term can quantitatively be calculated using the morphometric approach (MA) which expresses the term as the linear combinations of the four geometric measures of a solute and the corresponding coefficients determined with the energy representation (ER) method. Since the MA enables us to finish the computation of the solvent reorganization term in less than 0.1 s once the coefficients are determined, the use of the MA enables us to provide an efficient computation of the HFE even for large, complex solutes. Through the applications, we find that our method has almost the same quantitative performance as the ER method with substantial reduction of the computational load. PMID:25956125
Accurate calculation of computer-generated holograms using angular-spectrum layer-oriented method.
Zhao, Yan; Cao, Liangcai; Zhang, Hao; Kong, Dezhao; Jin, Guofan
2015-10-01
Fast calculation and correct depth cue are crucial issues in the calculation of computer-generated hologram (CGH) for high quality three-dimensional (3-D) display. An angular-spectrum based algorithm for layer-oriented CGH is proposed. Angular spectra from each layer are synthesized as a layer-corresponded sub-hologram based on the fast Fourier transform without paraxial approximation. The proposed method can avoid the huge computational cost of the point-oriented method and yield accurate predictions of the whole diffracted field compared with other layer-oriented methods. CGHs of versatile formats of 3-D digital scenes, including computed tomography and 3-D digital models, are demonstrated with precise depth performance and advanced image quality. PMID:26480062
Time accurate application of the MacCormack 2-4 scheme on massively parallel computers
NASA Technical Reports Server (NTRS)
Hudson, Dale A.; Long, Lyle N.
1995-01-01
Many recent computational efforts in turbulence and acoustics research have used higher order numerical algorithms. One popular method has been the explicit MacCormack 2-4 scheme. The MacCormack 2-4 scheme is second order accurate in time and fourth order accurate in space, and is stable for CFL's below 2/3. Current research has shown that the method can give accurate results but does exhibit significant Gibbs phenomena at sharp discontinuities. The impact of adding Jameson type second, third, and fourth order artificial viscosity was examined here. Category 2 problems, the nonlinear traveling wave and the Riemann problem, were computed using a CFL number of 0.25. This research has found that dispersion errors can be significantly reduced or nearly eliminated by using a combination of second and third order terms in the damping. Use of second and fourth order terms reduced the magnitude of dispersion errors but not as effectively as the second and third order combination. The program was coded using Thinking Machine's CM Fortran, a variant of Fortran 90/High Performance Fortran, and was executed on a 2K CM-200. Simple extrapolation boundary conditions were used for both problems.
NASA Astrophysics Data System (ADS)
Peng, Liang-You; Gong, Qihuang
2010-12-01
The accurate computations of hydrogenic continuum wave functions are very important in many branches of physics such as electron-atom collisions, cold atom physics, and atomic ionization in strong laser fields, etc. Although there already exist various algorithms and codes, most of them are only reliable in a certain ranges of parameters. In some practical applications, accurate continuum wave functions need to be calculated at extremely low energies, large radial distances and/or large angular momentum number. Here we provide such a code, which can generate accurate hydrogenic continuum wave functions and corresponding Coulomb phase shifts at a wide range of parameters. Without any essential restrict to angular momentum number, the present code is able to give reliable results at the electron energy range [10,10] eV for radial distances of [10,10] a.u. We also find the present code is very efficient, which should find numerous applications in many fields such as strong field physics. Program summaryProgram title: HContinuumGautchi Catalogue identifier: AEHD_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHD_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1233 No. of bytes in distributed program, including test data, etc.: 7405 Distribution format: tar.gz Programming language: Fortran90 in fixed format Computer: AMD Processors Operating system: Linux RAM: 20 MBytes Classification: 2.7, 4.5 Nature of problem: The accurate computation of atomic continuum wave functions is very important in many research fields such as strong field physics and cold atom physics. Although there have already existed various algorithms and codes, most of them can only be applicable and reliable in a certain range of parameters. We present here an accurate FORTRAN program for
A particle-tracking approach for accurate material derivative measurements with tomographic PIV
NASA Astrophysics Data System (ADS)
Novara, Matteo; Scarano, Fulvio
2013-08-01
The evaluation of the instantaneous 3D pressure field from tomographic PIV data relies on the accurate estimate of the fluid velocity material derivative, i.e., the velocity time rate of change following a given fluid element. To date, techniques that reconstruct the fluid parcel trajectory from a time sequence of 3D velocity fields obtained with Tomo-PIV have already been introduced. However, an accurate evaluation of the fluid element acceleration requires trajectory reconstruction over a relatively long observation time, which reduces random errors. On the other hand, simple integration and finite difference techniques suffer from increasing truncation errors when complex trajectories need to be reconstructed over a long time interval. In principle, particle-tracking velocimetry techniques (3D-PTV) enable the accurate reconstruction of single particle trajectories over a long observation time. Nevertheless, PTV can be reliably performed only at limited particle image number density due to errors caused by overlapping particles. The particle image density can be substantially increased by use of tomographic PIV. In the present study, a technique to combine the higher information density of tomographic PIV and the accurate trajectory reconstruction of PTV is proposed (Tomo-3D-PTV). The particle-tracking algorithm is applied to the tracers detected in the 3D domain obtained by tomographic reconstruction. The 3D particle information is highly sparse and intersection of trajectories is virtually impossible. As a result, ambiguities in the particle path identification over subsequent recordings are easily avoided. Polynomial fitting functions are introduced that describe the particle position in time with sequences based on several recordings, leading to the reduction in truncation errors for complex trajectories. Moreover, the polynomial regression approach provides a reduction in the random errors due to the particle position measurement. Finally, the acceleration
Gantz, Daniel T; Gantz, Donald T; Walch, Mark A; Roberts, Maria Antonia; Buscaglia, JoAnn
2014-12-01
A novel approach to automated fingerprint matching and scoring that produces accurate locally and nonlinearly adjusted overlays of a latent print onto each reference print in a corpus is described. The technology, which addresses challenges inherent to latent prints, provides the latent print examiner with a prioritized ranking of candidate reference prints based on the overlays of the latent onto each candidate print. In addition to supporting current latent print comparison practices, this approach can make it possible to return a greater number of AFIS candidate prints because the ranked overlays provide a substantial starting point for latent-to-reference print comparison. To provide the image information required to create an accurate overlay of a latent print onto a reference print, "Ridge-Specific Markers" (RSMs), which correspond to short continuous segments of a ridge or furrow, are introduced. RSMs are reliably associated with any specific local section of a ridge or a furrow using the geometric information available from the image. Latent prints are commonly fragmentary, with reduced clarity and limited minutiae (i.e., ridge endings and bifurcations). Even in the absence of traditional minutiae, latent prints contain very important information in their ridges that permit automated matching using RSMs. No print orientation or information beyond the RSMs is required to generate the overlays. This automated process is applied to the 88 good quality latent prints in the NIST Special Database (SD) 27. Nonlinear overlays of each latent were produced onto all of the 88 reference prints in the NIST SD27. With fully automated processing, the true mate reference prints were ranked in the first candidate position for 80.7% of the latents tested, and 89.8% of the true mate reference prints ranked in the top ten positions. After manual post-processing of those latents for which the true mate reference print was not ranked first, these frequencies increased to 90
Time-accurate Navier-Stokes computations of classical two-dimensional edge tone flow fields
NASA Technical Reports Server (NTRS)
Liu, B. L.; O'Farrell, J. M.; Jones, Jess H.
1990-01-01
Time-accurate Navier-Stokes computations were performed to study a Class II (acoustic) whistle, the edge tone, and gain knowledge of the vortex-acoustic coupling mechanisms driving production of these tones. Results were obtained by solving the full Navier-Stokes equations for laminar compressible air flow of a two-dimensional jet issuing from a slit interacting with a wedge. Cases considered were determined by varying the distance from the slit to the edge. Flow speed was kept constant at 1750 cm/sec as was the slit thickness of 0.1 cm, corresponding to conditions in the experiments of Brown. Excellent agreement was obtained in all four edge tone stage cases between the present computational results and the experimentally obtained results of Brown. Specific edge tone generated phenomena and further confirmation of certain theories concerning these phenomena were brought to light in this analytical simulation of edge tones.
NASA Astrophysics Data System (ADS)
Meyer, Daniel W.; Jenny, Patrick
2013-08-01
Different simulation methods are applicable to study turbulent mixing. When applying probability density function (PDF) methods, turbulent transport, and chemical reactions appear in closed form, which is not the case in second moment closure methods (RANS). Moreover, PDF methods provide the entire joint velocity-scalar PDF instead of a limited set of moments. In PDF methods, however, a mixing model is required to account for molecular diffusion. In joint velocity-scalar PDF methods, mixing models should also account for the joint velocity-scalar statistics, which is often under appreciated in applications. The interaction by exchange with the conditional mean (IECM) model accounts for these joint statistics, but requires velocity-conditional scalar means that are expensive to compute in spatially three dimensional settings. In this work, two alternative mixing models are presented that provide more accurate PDF predictions at reduced computational cost compared to the IECM model, since no conditional moments have to be computed. All models are tested for different mixing benchmark cases and their computational efficiencies are inspected thoroughly. The benchmark cases involve statistically homogeneous and inhomogeneous settings dealing with three streams that are characterized by two passive scalars. The inhomogeneous case clearly illustrates the importance of accounting for joint velocity-scalar statistics in the mixing model. Failure to do so leads to significant errors in the resulting scalar means, variances and other statistics.
Simple but accurate GCM-free approach for quantifying anthropogenic climate change
NASA Astrophysics Data System (ADS)
Lovejoy, S.
2014-12-01
We are so used to analysing the climate with the help of giant computer models (GCM's) that it is easy to get the impression that they are indispensable. Yet anthropogenic warming is so large (roughly 0.9oC) that it turns out that it is straightforward to quantify it with more empirically based methodologies that can be readily understood by the layperson. The key is to use the CO2 forcing as a linear surrogate for all the anthropogenic effects from 1880 to the present (implicitly including all effects due to Greenhouse Gases, aerosols and land use changes). To a good approximation, double the economic activity, double the effects. The relationship between the forcing and global mean temperature is extremely linear as can be seen graphically and understood without fancy statistics, [Lovejoy, 2014a] (see the attached figure and http://www.physics.mcgill.ca/~gang/Lovejoy.htm). To an excellent approximation, the deviations from the linear forcing - temperature relation can be interpreted as the natural variability. For example, this direct - yet accurate approach makes it graphically obvious that the "pause" or "hiatus" in the warming since 1998 is simply a natural cooling event that has roughly offset the anthropogenic warming [Lovejoy, 2014b]. Rather than trying to prove that the warming is anthropogenic, with a little extra work (and some nonlinear geophysics theory and pre-industrial multiproxies) we can disprove the competing theory that it is natural. This approach leads to the estimate that the probability of the industrial scale warming being a giant natural fluctuation is ≈0.1%: it can be dismissed. This destroys the last climate skeptic argument - that the models are wrong and the warming is natural. It finally allows for a closure of the debate. In this talk we argue that this new, direct, simple, intuitive approach provides an indispensable tool for communicating - and convincing - the public of both the reality and the amplitude of anthropogenic warming
An Accurate Method for Computing the Absorption of Solar Radiation by Water Vapor
NASA Technical Reports Server (NTRS)
Chou, M. D.
1980-01-01
The method is based upon molecular line parameters and makes use of a far wing scaling approximation and k distribution approach previously applied to the computation of the infrared cooling rate due to water vapor. Taking into account the wave number dependence of the incident solar flux, the solar heating rate is computed for the entire water vapor spectrum and for individual absorption bands. The accuracy of the method is tested against line by line calculations. The method introduces a maximum error of 0.06 C/day. The method has the additional advantage over previous methods in that it can be applied to any portion of the spectral region containing the water vapor bands. The integrated absorptances and line intensities computed from the molecular line parameters were compared with laboratory measurements. The comparison reveals that, among the three different sources, absorptance is the largest for the laboratory measurements.
Li, Kui; Wang, Lei; Lv, Yanhong; Gao, Pengyu; Song, Tianxiao
2015-01-01
Getting a land vehicle’s accurate position, azimuth and attitude rapidly is significant for vehicle based weapons’ combat effectiveness. In this paper, a new approach to acquire vehicle’s accurate position and orientation is proposed. It uses biaxial optical detection platform (BODP) to aim at and lock in no less than three pre-set cooperative targets, whose accurate positions are measured beforehand. Then, it calculates the vehicle’s accurate position, azimuth and attitudes by the rough position and orientation provided by vehicle based navigation systems and no less than three couples of azimuth and pitch angles measured by BODP. The proposed approach does not depend on Global Navigation Satellite System (GNSS), thus it is autonomous and difficult to interfere. Meanwhile, it only needs a rough position and orientation as algorithm’s iterative initial value, consequently, it does not have high performance requirement for Inertial Navigation System (INS), odometer and other vehicle based navigation systems, even in high precise applications. This paper described the system’s working procedure, presented theoretical deviation of the algorithm, and then verified its effectiveness through simulation and vehicle experiments. The simulation and experimental results indicate that the proposed approach can achieve positioning and orientation accuracy of 0.2 m and 20″ respectively in less than 3 min. PMID:26492249
Li, Kui; Wang, Lei; Lv, Yanhong; Gao, Pengyu; Song, Tianxiao
2015-01-01
Getting a land vehicle's accurate position, azimuth and attitude rapidly is significant for vehicle based weapons' combat effectiveness. In this paper, a new approach to acquire vehicle's accurate position and orientation is proposed. It uses biaxial optical detection platform (BODP) to aim at and lock in no less than three pre-set cooperative targets, whose accurate positions are measured beforehand. Then, it calculates the vehicle's accurate position, azimuth and attitudes by the rough position and orientation provided by vehicle based navigation systems and no less than three couples of azimuth and pitch angles measured by BODP. The proposed approach does not depend on Global Navigation Satellite System (GNSS), thus it is autonomous and difficult to interfere. Meanwhile, it only needs a rough position and orientation as algorithm's iterative initial value, consequently, it does not have high performance requirement for Inertial Navigation System (INS), odometer and other vehicle based navigation systems, even in high precise applications. This paper described the system's working procedure, presented theoretical deviation of the algorithm, and then verified its effectiveness through simulation and vehicle experiments. The simulation and experimental results indicate that the proposed approach can achieve positioning and orientation accuracy of 0.2 m and 20″ respectively in less than 3 min. PMID:26492249
Franck, Christopher T; Koffarnus, Mikhail N; House, Leanna L; Bickel, Warren K
2015-01-01
The study of delay discounting, or valuation of future rewards as a function of delay, has contributed to understanding the behavioral economics of addiction. Accurate characterization of discounting can be furthered by statistical model selection given that many functions have been proposed to measure future valuation of rewards. The present study provides a convenient Bayesian model selection algorithm that selects the most probable discounting model among a set of candidate models chosen by the researcher. The approach assigns the most probable model for each individual subject. Importantly, effective delay 50 (ED50) functions as a suitable unifying measure that is computable for and comparable between a number of popular functions, including both one- and two-parameter models. The combined model selection/ED50 approach is illustrated using empirical discounting data collected from a sample of 111 undergraduate students with models proposed by Laibson (1997); Mazur (1987); Myerson & Green (1995); Rachlin (2006); and Samuelson (1937). Computer simulation suggests that the proposed Bayesian model selection approach outperforms the single model approach when data truly arise from multiple models. When a single model underlies all participant data, the simulation suggests that the proposed approach fares no worse than the single model approach.
Computational approaches in modeling spectra of biological chromophores
NASA Astrophysics Data System (ADS)
Nemukhin, Alexander V.; Grigorenko, Bella L.; Bochenkova, Anastasia V.; Bravaya, Ksenia B.; Savitsky, Alexander P.
2008-02-01
Computational approaches to describe optical spectra of biological chromophores in proteins, in solutions and in the gas phase are discussed. Recently, accurate measurements of spectral properties for the series of chromophores in different media allowed the authors to estimate the positions of the bands with a high accuracy and to challenge theoreticians by stating that the measured S 0-S I transition wavelengths may be used as new benchmark values for the theory. The novel computational approaches based on the multiconfigurational quasidegenerate perturbation theory present the practical means how to adapt the high level methodology for calculations of accurate excitation energies in large biological chromophores. The theory is illustrated for a series of model compounds for which experimental data are available: the retinal molecule in the protonated Shiff-base form, the chromophores from the Green Fluorescent Protein family including the kindling protein asFP595, and the chromophore from the BLUF domain containing photoreceptor proteins.
Computational approaches for systems metabolomics.
Krumsiek, Jan; Bartel, Jörg; Theis, Fabian J
2016-06-01
Systems genetics is defined as the simultaneous assessment and analysis of multi-omics datasets. In the past few years, metabolomics has been established as a robust tool describing an important functional layer in this approach. The metabolome of a biological system represents an integrated state of genetic and environmental factors and has been referred to as a 'link between genotype and phenotype'. In this review, we summarize recent progresses in statistical analysis methods for metabolomics data in combination with other omics layers. We put a special focus on complex, multivariate statistical approaches as well as pathway-based and network-based analysis methods. Moreover, we outline current challenges and pitfalls of metabolomics-focused multi-omics analyses and discuss future steps for the field.
Application of the accurate mass and time tag approach in studies of the human blood lipidome
Ding, Jie; Sorensen, Christina M.; Jaitly, Navdeep; Jiang, Hongliang; Orton, Daniel J.; Monroe, Matthew E.; Moore, Ronald J.; Smith, Richard D.; Metz, Thomas O.
2008-08-15
We report a preliminary demonstration of the accurate mass and time (AMT) tag approach for lipidomics. Initial data-dependent LC-MS/MS analyses of human plasma, erythrocyte, and lymphocyte lipids were performed in order to identify lipid molecular species in conjunction with complementary accurate mass and isotopic distribution information. Identified lipids were used to populate initial lipid AMT tag databases containing 250 and 45 entries for those species detected in positive and negative electrospray ionization (ESI) modes, respectively. The positive ESI database was then utilized to identify human plasma, erythrocyte, and lymphocyte lipids in high-throughput quantitative LC-MS analyses based on the AMT tag approach. We were able to define the lipid profiles of human plasma, erythrocytes, and lymphocytes based on qualitative and quantitative differences in lipid abundance. In addition, we also report on the optimization of a reversed-phase LC method for the separation of lipids in these sample types.
Finding accurate frontiers: A knowledge-intensive approach to relational learning
NASA Technical Reports Server (NTRS)
Pazzani, Michael; Brunk, Clifford
1994-01-01
An approach to analytic learning is described that searches for accurate entailments of a Horn Clause domain theory. A hill-climbing search, guided by an information based evaluation function, is performed by applying a set of operators that derive frontiers from domain theories. The analytic learning system is one component of a multi-strategy relational learning system. We compare the accuracy of concepts learned with this analytic strategy to concepts learned with an analytic strategy that operationalizes the domain theory.
Time-Accurate Computation of Viscous Flow Around Deforming Bodies Using Overset Grids
Fast, P; Henshaw, W D
2001-04-02
Dynamically evolving boundaries and deforming bodies interacting with a flow are commonly encountered in fluid dynamics. However, the numerical simulation of flows with dynamic boundaries is difficult with current methods. We propose a new method for studying such problems. The key idea is to use the overset grid method with a thin, body-fitted grid near the deforming boundary, while using fixed Cartesian grids to cover most of the computational domain. Our approach combines the strengths of earlier moving overset grid methods for rigid body motion, and unstructured grid methods for Aow-structure interactions. Large scale deformation of the flow boundaries can be handled without a global regridding, and in a computationally efficient way. In terms of computational cost, even a full overset grid regridding is significantly cheaper than a full regridding of an unstructured grid for the same domain, especially in three dimensions. Numerical studies are used to verify accuracy and convergence of our flow solver. As a computational example, we consider two-dimensional incompressible flow past a flexible filament with prescribed dynamics.
When do perturbative approaches accurately capture the dynamics of complex quantum systems?
NASA Astrophysics Data System (ADS)
Fruchtman, Amir; Lambert, Neill; Gauger, Erik M.
2016-06-01
Understanding the dynamics of higher-dimensional quantum systems embedded in a complex environment remains a significant theoretical challenge. While several approaches yielding numerically converged solutions exist, these are computationally expensive and often provide only limited physical insight. Here we address the question: when do more intuitive and simpler-to-compute second-order perturbative approaches provide adequate accuracy? We develop a simple analytical criterion and verify its validity for the case of the much-studied FMO dynamics as well as the canonical spin-boson model.
When do perturbative approaches accurately capture the dynamics of complex quantum systems?
Fruchtman, Amir; Lambert, Neill; Gauger, Erik M.
2016-01-01
Understanding the dynamics of higher-dimensional quantum systems embedded in a complex environment remains a significant theoretical challenge. While several approaches yielding numerically converged solutions exist, these are computationally expensive and often provide only limited physical insight. Here we address the question: when do more intuitive and simpler-to-compute second-order perturbative approaches provide adequate accuracy? We develop a simple analytical criterion and verify its validity for the case of the much-studied FMO dynamics as well as the canonical spin-boson model. PMID:27335176
Enabling fast, stable and accurate peridynamic computations using multi-time-step integration
Lindsay, P.; Parks, M. L.; Prakash, A.
2016-04-13
Peridynamics is a nonlocal extension of classical continuum mechanics that is well-suited for solving problems with discontinuities such as cracks. This paper extends the peridynamic formulation to decompose a problem domain into a number of smaller overlapping subdomains and to enable the use of different time steps in different subdomains. This approach allows regions of interest to be isolated and solved at a small time step for increased accuracy while the rest of the problem domain can be solved at a larger time step for greater computational efficiency. Lastly, performance of the proposed method in terms of stability, accuracy, andmore » computational cost is examined and several numerical examples are presented to corroborate the findings.« less
Quantitative approaches to computational vaccinology.
Doytchinova, Irini A; Flower, Darren R
2002-06-01
This article reviews the newly released JenPep database and two new powerful techniques for T-cell epitope prediction: (i) the additive method; and (ii) a 3D-Quantitative Structure Activity Relationships (3D-QSAR) method, based on Comparative Molecular Similarity Indices Analysis (CoMSIA). The JenPep database is a family of relational databases supporting the growing need of immunoinformaticians for quantitative data on peptide binding to major histocompatibility complexes and to the Transporters associated with Antigen Processing (TAP). It also contains an annotated list of T-cell epitopes. The database is available free via the Internet (http://www.jenner.ac.uk/JenPep). The additive prediction method is based on the assumption that the binding affinity of a peptide depends on the contributions from each amino acid as well as on the interactions between the adjacent and every second side-chain. In the 3D-QSAR approach, the influence of five physicochemical properties (steric bulk, electrostatic potential, local hydrophobicity, hydrogen-bond donor and hydrogen-bond acceptor abilities) on the affinity of peptides binding to MHC molecules were considered. Both methods were exemplified through their application to the well-studied problem of peptides binding to the human class I MHC molecule HLA-A*0201. PMID:12067414
Toward exascale computing through neuromorphic approaches.
James, Conrad D.
2010-09-01
While individual neurons function at relatively low firing rates, naturally-occurring nervous systems not only surpass manmade systems in computing power, but accomplish this feat using relatively little energy. It is asserted that the next major breakthrough in computing power will be achieved through application of neuromorphic approaches that mimic the mechanisms by which neural systems integrate and store massive quantities of data for real-time decision making. The proposed LDRD provides a conceptual foundation for SNL to make unique advances toward exascale computing. First, a team consisting of experts from the HPC, MESA, cognitive and biological sciences and nanotechnology domains will be coordinated to conduct an exercise with the outcome being a concept for applying neuromorphic computing to achieve exascale computing. It is anticipated that this concept will involve innovative extension and integration of SNL capabilities in MicroFab, material sciences, high-performance computing, and modeling and simulation of neural processes/systems.
Accurate computation of surface stresses and forces with immersed boundary methods
NASA Astrophysics Data System (ADS)
Goza, Andres; Liska, Sebastian; Morley, Benjamin; Colonius, Tim
2016-09-01
Many immersed boundary methods solve for surface stresses that impose the velocity boundary conditions on an immersed body. These surface stresses may contain spurious oscillations that make them ill-suited for representing the physical surface stresses on the body. Moreover, these inaccurate stresses often lead to unphysical oscillations in the history of integrated surface forces such as the coefficient of lift. While the errors in the surface stresses and forces do not necessarily affect the convergence of the velocity field, it is desirable, especially in fluid-structure interaction problems, to obtain smooth and convergent stress distributions on the surface. To this end, we show that the equation for the surface stresses is an integral equation of the first kind whose ill-posedness is the source of spurious oscillations in the stresses. We also demonstrate that for sufficiently smooth delta functions, the oscillations may be filtered out to obtain physically accurate surface stresses. The filtering is applied as a post-processing procedure, so that the convergence of the velocity field is unaffected. We demonstrate the efficacy of the method by computing stresses and forces that converge to the physical stresses and forces for several test problems.
Toward accurate tooth segmentation from computed tomography images using a hybrid level set model
Gan, Yangzhou; Zhao, Qunfei; Xia, Zeyang E-mail: jing.xiong@siat.ac.cn; Hu, Ying; Xiong, Jing E-mail: jing.xiong@siat.ac.cn; Zhang, Jianwei
2015-01-15
Purpose: A three-dimensional (3D) model of the teeth provides important information for orthodontic diagnosis and treatment planning. Tooth segmentation is an essential step in generating the 3D digital model from computed tomography (CT) images. The aim of this study is to develop an accurate and efficient tooth segmentation method from CT images. Methods: The 3D dental CT volumetric images are segmented slice by slice in a two-dimensional (2D) transverse plane. The 2D segmentation is composed of a manual initialization step and an automatic slice by slice segmentation step. In the manual initialization step, the user manually picks a starting slice and selects a seed point for each tooth in this slice. In the automatic slice segmentation step, a developed hybrid level set model is applied to segment tooth contours from each slice. Tooth contour propagation strategy is employed to initialize the level set function automatically. Cone beam CT (CBCT) images of two subjects were used to tune the parameters. Images of 16 additional subjects were used to validate the performance of the method. Volume overlap metrics and surface distance metrics were adopted to assess the segmentation accuracy quantitatively. The volume overlap metrics were volume difference (VD, mm{sup 3}) and Dice similarity coefficient (DSC, %). The surface distance metrics were average symmetric surface distance (ASSD, mm), RMS (root mean square) symmetric surface distance (RMSSSD, mm), and maximum symmetric surface distance (MSSD, mm). Computation time was recorded to assess the efficiency. The performance of the proposed method has been compared with two state-of-the-art methods. Results: For the tested CBCT images, the VD, DSC, ASSD, RMSSSD, and MSSD for the incisor were 38.16 ± 12.94 mm{sup 3}, 88.82 ± 2.14%, 0.29 ± 0.03 mm, 0.32 ± 0.08 mm, and 1.25 ± 0.58 mm, respectively; the VD, DSC, ASSD, RMSSSD, and MSSD for the canine were 49.12 ± 9.33 mm{sup 3}, 91.57 ± 0.82%, 0.27 ± 0.02 mm, 0
NASA Astrophysics Data System (ADS)
Ohkawauchi, K.; Takenaka, H.
2006-12-01
We propose a new method for the calculation of seismic wave propagation using the interpolated differential operator (IDO, Aoki,1997) which is a numerical method for solving the partial differential equations and is based on a high accurate interpolation of the profile for the independent variables over a local area. It improves the accuracy of wave computation with high accuracy because the local interpolation can represent high order behavior of wave field between grid points. In addition, locality of this approach makes possible treatment of boundary conditions exactly. In this study, we address computation of plane-wave responses of vertically heterogeneous structure models. We then solve the elastodynamic equation for plane wave derived by Tanaka and Takenaka (2005). The equations to be solved in our method are not only velocity-stress equations but also the corresponding ones integrated over each cell between adjacent grid points. We use two staggered-grid systems which can be non-uniform, and then discretize the governing equations using a finite-difference scheme of second-order accurate in time, and the second-order Hermite interpolation in space. In this method, the second-order Hermite interpolation of particle velocity or stress is obtained from the values at the adjacent two grid points and the integration value at the cell between the grid points. The time marching of the original and integrated quantities are proceeded, and in the following time step the quantities are computed on the alternative grid system to that used in the current time step. In implementation of a free-surface boundary condition, all field quantities locate just on the free surface. Their computational accuracy is the same order as those in the other spatial domain. We also implement the interface condition in a similarly way to the free surface condition. We used some simple models to test the scheme. The results showed that the waveforms calculated by our method fit the
Thermal Conductivities in Solids from First Principles: Accurate Computations and Rapid Estimates
NASA Astrophysics Data System (ADS)
Carbogno, Christian; Scheffler, Matthias
In spite of significant research efforts, a first-principles determination of the thermal conductivity κ at high temperatures has remained elusive. Boltzmann transport techniques that account for anharmonicity perturbatively become inaccurate under such conditions. Ab initio molecular dynamics (MD) techniques using the Green-Kubo (GK) formalism capture the full anharmonicity, but can become prohibitively costly to converge in time and size. We developed a formalism that accelerates such GK simulations by several orders of magnitude and that thus enables its application within the limited time and length scales accessible in ab initio MD. For this purpose, we determine the effective harmonic potential occurring during the MD, the associated temperature-dependent phonon properties and lifetimes. Interpolation in reciprocal and frequency space then allows to extrapolate to the macroscopic scale. For both force-field and ab initio MD, we validate this approach by computing κ for Si and ZrO2, two materials known for their particularly harmonic and anharmonic character. Eventually, we demonstrate how these techniques facilitate reasonable estimates of κ from existing MD calculations at virtually no additional computational cost.
Accurate electronic-structure description of Mn complexes: a GGA+U approach
NASA Astrophysics Data System (ADS)
Li, Elise Y.; Kulik, Heather; Marzari, Nicola
2008-03-01
Conventional density-functional approach often fail in offering an accurate description of the spin-resolved energetics in transition metals complexes. We will focus here on Mn complexes, where many aspects of the molecular structure and the reaction mechanisms are still unresolved - most notably in the oxygen-evolving complex (OEC) of photosystem II and the manganese catalase (MC). We apply a self-consistent GGA + U approach [1], originally designed within the DFT framework for the treatment of strongly correlated materials, to describe the geometry, the electronic and the magnetic properties of various manganese oxide complexes, finding very good agreement with higher-order ab-initio calculations. In particular, the different oxidation states of dinuclear systems containing the [Mn2O2]^n+ (n= 2, 3, 4) core are investigated, in order to mimic the basic face unit of the OEC complex. [1]. H. J. Kulik, M. Cococcioni, D. A. Scherlis, N. Marzari, Phys. Rev. Lett., 2006, 97, 103001
Stable, accurate and efficient computation of normal modes for horizontal stratified models
NASA Astrophysics Data System (ADS)
Wu, Bo; Chen, Xiaofei
2016-06-01
We propose an adaptive root-determining strategy that is very useful when dealing with trapped modes or Stoneley modes whose energies become very insignificant on the free surface in the presence of low-velocity layers or fluid layers in the model. Loss of modes in these cases or inaccuracy in the calculation of these modes may then be easily avoided. Built upon the generalized reflection/transmission coefficients, the concept of "family of secular functions" that we herein call "adaptive mode observers", is thus naturally introduced to implement this strategy, the underlying idea of which has been distinctly noted for the first time and may be generalized to other applications such as free oscillations or applied to other methods in use when these cases are encountered. Additionally, we have made further improvements upon the generalized reflection/transmission coefficient method; mode observers associated with only the free surface and low-velocity layers (and the fluid/solid interface if the model contains fluid layers) are adequate to guarantee no loss and high precision at the same time of any physically existent modes without excessive calculations. Finally, the conventional definition of the fundamental mode is reconsidered, which is entailed in the cases under study. Some computational aspects are remarked on. With the additional help afforded by our superior root-searching scheme and the possibility of speeding calculation using a less number of layers aided by the concept of "turning point", our algorithm is remarkably efficient as well as stable and accurate and can be used as a powerful tool for widely related applications.
Stable, accurate and efficient computation of normal modes for horizontal stratified models
NASA Astrophysics Data System (ADS)
Wu, Bo; Chen, Xiaofei
2016-08-01
We propose an adaptive root-determining strategy that is very useful when dealing with trapped modes or Stoneley modes whose energies become very insignificant on the free surface in the presence of low-velocity layers or fluid layers in the model. Loss of modes in these cases or inaccuracy in the calculation of these modes may then be easily avoided. Built upon the generalized reflection/transmission coefficients, the concept of `family of secular functions' that we herein call `adaptive mode observers' is thus naturally introduced to implement this strategy, the underlying idea of which has been distinctly noted for the first time and may be generalized to other applications such as free oscillations or applied to other methods in use when these cases are encountered. Additionally, we have made further improvements upon the generalized reflection/transmission coefficient method; mode observers associated with only the free surface and low-velocity layers (and the fluid/solid interface if the model contains fluid layers) are adequate to guarantee no loss and high precision at the same time of any physically existent modes without excessive calculations. Finally, the conventional definition of the fundamental mode is reconsidered, which is entailed in the cases under study. Some computational aspects are remarked on. With the additional help afforded by our superior root-searching scheme and the possibility of speeding calculation using a less number of layers aided by the concept of `turning point', our algorithm is remarkably efficient as well as stable and accurate and can be used as a powerful tool for widely related applications.
Computational Approaches to Study Microbes and Microbiomes
Greene, Casey S.; Foster, James A.; Stanton, Bruce A.; Hogan, Deborah A.; Bromberg, Yana
2016-01-01
Technological advances are making large-scale measurements of microbial communities commonplace. These newly acquired datasets are allowing researchers to ask and answer questions about the composition of microbial communities, the roles of members in these communities, and how genes and molecular pathways are regulated in individual community members and communities as a whole to effectively respond to diverse and changing environments. In addition to providing a more comprehensive survey of the microbial world, this new information allows for the development of computational approaches to model the processes underlying microbial systems. We anticipate that the field of computational microbiology will continue to grow rapidly in the coming years. In this manuscript we highlight both areas of particular interest in microbiology as well as computational approaches that begin to address these challenges. PMID:26776218
Tiwari, Saumya; Reddy, Vijaya B.; Bhargava, Rohit; Raman, Jaishankar
2015-01-01
Rejection is a common problem after cardiac transplants leading to significant number of adverse events and deaths, particularly in the first year of transplantation. The gold standard to identify rejection is endomyocardial biopsy. This technique is complex, cumbersome and requires a lot of expertise in the correct interpretation of stained biopsy sections. Traditional histopathology cannot be used actively or quickly during cardiac interventions or surgery. Our objective was to develop a stain-less approach using an emerging technology, Fourier transform infrared (FT-IR) spectroscopic imaging to identify different components of cardiac tissue by their chemical and molecular basis aided by computer recognition, rather than by visual examination using optical microscopy. We studied this technique in assessment of cardiac transplant rejection to evaluate efficacy in an example of complex cardiovascular pathology. We recorded data from human cardiac transplant patients’ biopsies, used a Bayesian classification protocol and developed a visualization scheme to observe chemical differences without the need of stains or human supervision. Using receiver operating characteristic curves, we observed probabilities of detection greater than 95% for four out of five histological classes at 10% probability of false alarm at the cellular level while correctly identifying samples with the hallmarks of the immune response in all cases. The efficacy of manual examination can be significantly increased by observing the inherent biochemical changes in tissues, which enables us to achieve greater diagnostic confidence in an automated, label-free manner. We developed a computational pathology system that gives high contrast images and seems superior to traditional staining procedures. This study is a prelude to the development of real time in situ imaging systems, which can assist interventionists and surgeons actively during procedures. PMID:25932912
NASA Technical Reports Server (NTRS)
Emmons, Louisa; De Zafra, Robert
1991-01-01
A simple method for milling accurate off-axis parabolic mirrors with a computer-controlled milling machine is discussed. For machines with a built-in circle-cutting routine, an exact paraboloid can be milled with few computer commands and without the use of the spherical or linear approximations. The proposed method can be adapted easily to cut off-axis sections of elliptical or spherical mirrors.
Computational Approach for Developing Blood Pump
NASA Technical Reports Server (NTRS)
Kwak, Dochan
2002-01-01
This viewgraph presentation provides an overview of the computational approach to developing a ventricular assist device (VAD) which utilizes NASA aerospace technology. The VAD is used as a temporary support to sick ventricles for those who suffer from late stage congestive heart failure (CHF). The need for donor hearts is much greater than their availability, and the VAD is seen as a bridge-to-transplant. The computational issues confronting the design of a more advanced, reliable VAD include the modelling of viscous incompressible flow. A computational approach provides the possibility of quantifying the flow characteristics, which is especially valuable for analyzing compact design with highly sensitive operating conditions. Computational fluid dynamics (CFD) and rocket engine technology has been applied to modify the design of a VAD which enabled human transplantation. The computing requirement for this project is still large, however, and the unsteady analysis of the entire system from natural heart to aorta involves several hundred revolutions of the impeller. Further study is needed to assess the impact of mechanical VADs on the human body
Approach to constructing reconfigurable computer vision system
NASA Astrophysics Data System (ADS)
Xue, Jianru; Zheng, Nanning; Wang, Xiaoling; Zhang, Yongping
2000-10-01
In this paper, we propose an approach to constructing reconfigurable vision system. We found that timely and efficient execution of early tasks can significantly enhance the performance of whole computer vision tasks, and abstract out a set of basic, computationally intensive stream operations that may be performed in parallel and embodies them in a series of specific front-end processors. These processors which based on FPGAs (Field programmable gate arrays) can be re-programmable to permit a range of different types of feature maps, such as edge detection & linking, image filtering. Front-end processors and a powerful DSP constitute a computing platform which can perform many CV tasks. Additionally we adopt the focus-of-attention technologies to reduce the I/O and computational demands by performing early vision processing only within a particular region of interest. Then we implement a multi-page, dual-ported image memory interface between the image input and computing platform (including front-end processors, DSP). Early vision features were loaded into banks of dual-ported image memory arrays, which are continually raster scan updated at high speed from the input image or video data stream. Moreover, the computing platform can be complete asynchronous, random access to the image data or any other early vision feature maps through the dual-ported memory banks. In this way, the computing platform resources can be properly allocated to a region of interest and decoupled from the task of dealing with a high speed serial raster scan input. Finally, we choose PCI Bus as the main channel between the PC and computing platform. Consequently, front-end processors' control registers and DSP's program memory were mapped into the PC's memory space, which provides user access to reconfigure the system at any time. We also present test result of a computer vision application based on the system.
Ustinov, E A
2014-10-01
Commensurate-incommensurate (C-IC) transition of krypton molecular layer on graphite received much attention in recent decades in theoretical and experimental researches. However, there still exists a possibility of generalization of the phenomenon from thermodynamic viewpoint on the basis of accurate molecular simulation. Recently, a new technique was developed for analysis of two-dimensional (2D) phase transitions in systems involving a crystalline phase, which is based on accounting for the effect of temperature and the chemical potential on the lattice constant of the 2D layer using the Gibbs-Duhem equation [E. A. Ustinov, J. Chem. Phys. 140, 074706 (2014)]. The technique has allowed for determination of phase diagrams of 2D argon layers on the uniform surface and in slit pores. This paper extends the developed methodology on systems accounting for the periodic modulation of the substrate potential. The main advantage of the developed approach is that it provides highly accurate evaluation of the chemical potential of crystalline layers, which allows reliable determination of temperature and other parameters of various 2D phase transitions. Applicability of the methodology is demonstrated on the krypton-graphite system. Analysis of phase diagram of the krypton molecular layer, thermodynamic functions of coexisting phases, and a method of prediction of adsorption isotherms is considered accounting for a compression of the graphite due to the krypton-carbon interaction. The temperature and heat of C-IC transition has been reliably determined for the gas-solid and solid-solid system.
Ustinov, E. A.
2014-10-07
Commensurate–incommensurate (C-IC) transition of krypton molecular layer on graphite received much attention in recent decades in theoretical and experimental researches. However, there still exists a possibility of generalization of the phenomenon from thermodynamic viewpoint on the basis of accurate molecular simulation. Recently, a new technique was developed for analysis of two-dimensional (2D) phase transitions in systems involving a crystalline phase, which is based on accounting for the effect of temperature and the chemical potential on the lattice constant of the 2D layer using the Gibbs–Duhem equation [E. A. Ustinov, J. Chem. Phys. 140, 074706 (2014)]. The technique has allowed for determination of phase diagrams of 2D argon layers on the uniform surface and in slit pores. This paper extends the developed methodology on systems accounting for the periodic modulation of the substrate potential. The main advantage of the developed approach is that it provides highly accurate evaluation of the chemical potential of crystalline layers, which allows reliable determination of temperature and other parameters of various 2D phase transitions. Applicability of the methodology is demonstrated on the krypton–graphite system. Analysis of phase diagram of the krypton molecular layer, thermodynamic functions of coexisting phases, and a method of prediction of adsorption isotherms is considered accounting for a compression of the graphite due to the krypton–carbon interaction. The temperature and heat of C-IC transition has been reliably determined for the gas–solid and solid–solid system.
NASA Astrophysics Data System (ADS)
Omori, Takayuki; Sano, Katsuhiro; Yoneda, Minoru
2014-05-01
This paper presents new correction approaches for "early" radiocarbon ages to reconstruct the Paleolithic absolute chronology. In order to discuss time-space distribution about the replacement of archaic humans, including Neanderthals in Europe, by the modern humans, a massive data, which covers a wide-area, would be needed. Today, some radiocarbon databases focused on the Paleolithic have been published and used for chronological studies. From a viewpoint of current analytical technology, however, the any database have unreliable results that make interpretation of radiocarbon dates difficult. Most of these unreliable ages had been published in the early days of radiocarbon analysis. In recent years, new analytical methods to determine highly-accurate dates have been developed. Ultrafiltration and ABOx-SC methods, as new sample pretreatments for bone and charcoal respectively, have attracted attention because they could remove imperceptible contaminates and derive reliable accurately ages. In order to evaluate the reliability of "early" data, we investigated the differences and variabilities of radiocarbon ages on different pretreatments, and attempted to develop correction functions for the assessment of the reliability. It can be expected that reliability of the corrected age is increased and the age applied to chronological research together with recent ages. Here, we introduce the methodological frameworks and archaeological applications.
Ustinov, E A
2014-10-01
Commensurate-incommensurate (C-IC) transition of krypton molecular layer on graphite received much attention in recent decades in theoretical and experimental researches. However, there still exists a possibility of generalization of the phenomenon from thermodynamic viewpoint on the basis of accurate molecular simulation. Recently, a new technique was developed for analysis of two-dimensional (2D) phase transitions in systems involving a crystalline phase, which is based on accounting for the effect of temperature and the chemical potential on the lattice constant of the 2D layer using the Gibbs-Duhem equation [E. A. Ustinov, J. Chem. Phys. 140, 074706 (2014)]. The technique has allowed for determination of phase diagrams of 2D argon layers on the uniform surface and in slit pores. This paper extends the developed methodology on systems accounting for the periodic modulation of the substrate potential. The main advantage of the developed approach is that it provides highly accurate evaluation of the chemical potential of crystalline layers, which allows reliable determination of temperature and other parameters of various 2D phase transitions. Applicability of the methodology is demonstrated on the krypton-graphite system. Analysis of phase diagram of the krypton molecular layer, thermodynamic functions of coexisting phases, and a method of prediction of adsorption isotherms is considered accounting for a compression of the graphite due to the krypton-carbon interaction. The temperature and heat of C-IC transition has been reliably determined for the gas-solid and solid-solid system. PMID:25296827
A Maximum-Entropy approach for accurate document annotation in the biomedical domain.
Tsatsaronis, George; Macari, Natalia; Torge, Sunna; Dietze, Heiko; Schroeder, Michael
2012-01-01
The increasing number of scientific literature on the Web and the absence of efficient tools used for classifying and searching the documents are the two most important factors that influence the speed of the search and the quality of the results. Previous studies have shown that the usage of ontologies makes it possible to process document and query information at the semantic level, which greatly improves the search for the relevant information and makes one step further towards the Semantic Web. A fundamental step in these approaches is the annotation of documents with ontology concepts, which can also be seen as a classification task. In this paper we address this issue for the biomedical domain and present a new automated and robust method, based on a Maximum Entropy approach, for annotating biomedical literature documents with terms from the Medical Subject Headings (MeSH).The experimental evaluation shows that the suggested Maximum Entropy approach for annotating biomedical documents with MeSH terms is highly accurate, robust to the ambiguity of terms, and can provide very good performance even when a very small number of training documents is used. More precisely, we show that the proposed algorithm obtained an average F-measure of 92.4% (precision 99.41%, recall 86.77%) for the full range of the explored terms (4,078 MeSH terms), and that the algorithm's performance is resilient to terms' ambiguity, achieving an average F-measure of 92.42% (precision 99.32%, recall 86.87%) in the explored MeSH terms which were found to be ambiguous according to the Unified Medical Language System (UMLS) thesaurus. Finally, we compared the results of the suggested methodology with a Naive Bayes and a Decision Trees classification approach, and we show that the Maximum Entropy based approach performed with higher F-Measure in both ambiguous and monosemous MeSH terms.
NASA Astrophysics Data System (ADS)
Park, Min-Chul; Leportier, Thibault; Kim, Wooshik; Song, Jindong
2016-06-01
In this paper, we present a method to characterize not only shape but also depth of defects in line and space mask patterns. Features in a mask are too fine for conventional imaging system to resolve them and coherent imaging system providing only the pattern diffracted by the mask are used. Then, phase retrieval methods may be applied, but the accuracy it too low to determine the exact shape of the defect. Deterministic methods have been proposed to characterize accurately the defect, but it requires a reference pattern. We propose to use successively phase retrieval algorithm to retrieve the general shape of the mask and then deterministic approach to characterize precisely the defects detected.
Oksel, Ceyda; Winkler, David A; Ma, Cai Y; Wilkins, Terry; Wang, Xue Z
2016-09-01
The number of engineered nanomaterials (ENMs) being exploited commercially is growing rapidly, due to the novel properties they exhibit. Clearly, it is important to understand and minimize any risks to health or the environment posed by the presence of ENMs. Data-driven models that decode the relationships between the biological activities of ENMs and their physicochemical characteristics provide an attractive means of maximizing the value of scarce and expensive experimental data. Although such structure-activity relationship (SAR) methods have become very useful tools for modelling nanotoxicity endpoints (nanoSAR), they have limited robustness and predictivity and, most importantly, interpretation of the models they generate is often very difficult. New computational modelling tools or new ways of using existing tools are required to model the relatively sparse and sometimes lower quality data on the biological effects of ENMs. The most commonly used SAR modelling methods work best with large datasets, are not particularly good at feature selection, can be relatively opaque to interpretation, and may not account for nonlinearity in the structure-property relationships. To overcome these limitations, we describe the application of a novel algorithm, a genetic programming-based decision tree construction tool (GPTree) to nanoSAR modelling. We demonstrate the use of GPTree in the construction of accurate and interpretable nanoSAR models by applying it to four diverse literature datasets. We describe the algorithm and compare model results across the four studies. We show that GPTree generates models with accuracies equivalent to or superior to those of prior modelling studies on the same datasets. GPTree is a robust, automatic method for generation of accurate nanoSAR models with important advantages that it works with small datasets, automatically selects descriptors, and provides significantly improved interpretability of models.
Fortenberry, Ryan C; Huang, Xinchuan; Schwenke, David W; Lee, Timothy J
2014-02-01
In this work, computational procedures are employed to compute the rotational and rovibrational spectra and line lists for H2O, CO2, and SO2. Building on the established use of quartic force fields, MP2 and CCSD(T) Dipole Moment Surfaces (DMSs) are computed for each system of study in order to produce line intensities as well as the transition energies. The computed results exhibit a clear correlation to reference data available in the HITRAN database. Additionally, even though CCSD(T) DMSs produce more accurate intensities as compared to experiment, the use of MP2 DMSs results in reliable line lists that are still comparable to experiment. The use of the less computationally costly MP2 method is beneficial in the study of larger systems where use of CCSD(T) would be more costly. PMID:23692860
A multi-objective optimization approach accurately resolves protein domain architectures
Bernardes, J.S.; Vieira, F.R.J.; Zaverucha, G.; Carbone, A.
2016-01-01
Motivation: Given a protein sequence and a number of potential domains matching it, what are the domain content and the most likely domain architecture for the sequence? This problem is of fundamental importance in protein annotation, constituting one of the main steps of all predictive annotation strategies. On the other hand, when potential domains are several and in conflict because of overlapping domain boundaries, finding a solution for the problem might become difficult. An accurate prediction of the domain architecture of a multi-domain protein provides important information for function prediction, comparative genomics and molecular evolution. Results: We developed DAMA (Domain Annotation by a Multi-objective Approach), a novel approach that identifies architectures through a multi-objective optimization algorithm combining scores of domain matches, previously observed multi-domain co-occurrence and domain overlapping. DAMA has been validated on a known benchmark dataset based on CATH structural domain assignments and on the set of Plasmodium falciparum proteins. When compared with existing tools on both datasets, it outperforms all of them. Availability and implementation: DAMA software is implemented in C++ and the source code can be found at http://www.lcqb.upmc.fr/DAMA. Contact: juliana.silva_bernardes@upmc.fr or alessandra.carbone@lip6.fr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26458889
A Novel PCR-Based Approach for Accurate Identification of Vibrio parahaemolyticus.
Li, Ruichao; Chiou, Jiachi; Chan, Edward Wai-Chi; Chen, Sheng
2016-01-01
A PCR-based assay was developed for more accurate identification of Vibrio parahaemolyticus through targeting the bla CARB-17 like element, an intrinsic β-lactamase gene that may also be regarded as a novel species-specific genetic marker of this organism. Homologous analysis showed that bla CARB-17 like genes were more conservative than the tlh, toxR and atpA genes, the genetic markers commonly used as detection targets in identification of V. parahaemolyticus. Our data showed that this bla CARB-17-specific PCR-based detection approach consistently achieved 100% specificity, whereas PCR targeting the tlh and atpA genes occasionally produced false positive results. Furthermore, a positive result of this test is consistently associated with an intrinsic ampicillin resistance phenotype of the test organism, presumably conferred by the products of bla CARB-17 like genes. We envision that combined analysis of the unique genetic and phenotypic characteristics conferred by bla CARB-17 shall further enhance the detection specificity of this novel yet easy-to-use detection approach to a level superior to the conventional methods used in V. parahaemolyticus detection and identification. PMID:26858713
A Novel PCR-Based Approach for Accurate Identification of Vibrio parahaemolyticus
Li, Ruichao; Chiou, Jiachi; Chan, Edward Wai-Chi; Chen, Sheng
2016-01-01
A PCR-based assay was developed for more accurate identification of Vibrio parahaemolyticus through targeting the blaCARB-17 like element, an intrinsic β-lactamase gene that may also be regarded as a novel species-specific genetic marker of this organism. Homologous analysis showed that blaCARB-17 like genes were more conservative than the tlh, toxR and atpA genes, the genetic markers commonly used as detection targets in identification of V. parahaemolyticus. Our data showed that this blaCARB-17-specific PCR-based detection approach consistently achieved 100% specificity, whereas PCR targeting the tlh and atpA genes occasionally produced false positive results. Furthermore, a positive result of this test is consistently associated with an intrinsic ampicillin resistance phenotype of the test organism, presumably conferred by the products of blaCARB-17 like genes. We envision that combined analysis of the unique genetic and phenotypic characteristics conferred by blaCARB-17 shall further enhance the detection specificity of this novel yet easy-to-use detection approach to a level superior to the conventional methods used in V. parahaemolyticus detection and identification. PMID:26858713
Esque, Jeremy; Cecchini, Marco
2015-04-23
The calculation of the free energy of conformation is key to understanding the function of biomolecules and has attracted significant interest in recent years. Here, we present an improvement of the confinement method that was designed for use in the context of explicit solvent MD simulations. The development involves an additional step in which the solvation free energy of the harmonically restrained conformers is accurately determined by multistage free energy perturbation simulations. As a test-case application, the newly introduced confinement/solvation free energy (CSF) approach was used to compute differences in free energy between conformers of the alanine dipeptide in explicit water. The results are in excellent agreement with reference calculations based on both converged molecular dynamics and umbrella sampling. To illustrate the general applicability of the method, conformational equilibria of met-enkephalin (5 aa) and deca-alanine (10 aa) in solution were also analyzed. In both cases, smoothly converged free-energy results were obtained in agreement with equilibrium sampling or literature calculations. These results demonstrate that the CSF method may provide conformational free-energy differences of biomolecules with small statistical errors (below 0.5 kcal/mol) and at a moderate computational cost even with a full representation of the solvent.
Digital test signal generation: An accurate SNR calibration approach for the DSN
NASA Technical Reports Server (NTRS)
Gutierrez-Luaces, Benito O.
1993-01-01
In support of the on-going automation of the Deep Space Network (DSN) a new method of generating analog test signals with accurate signal-to-noise ratio (SNR) is described. High accuracy is obtained by simultaneous generation of digital noise and signal spectra at the desired bandwidth (base-band or bandpass). The digital synthesis provides a test signal embedded in noise with the statistical properties of a stationary random process. Accuracy is dependent on test integration time and limited only by the system quantization noise (0.02 dB). The monitor and control as well as signal-processing programs reside in a personal computer (PC). Commands are transmitted to properly configure the specially designed high-speed digital hardware. The prototype can generate either two data channels modulated or not on a subcarrier, or one QPSK channel, or a residual carrier with one biphase data channel. The analog spectrum generated is on the DC to 10 MHz frequency range. These spectra may be up-converted to any desired frequency without loss on the characteristics of the SNR provided. Test results are presented.
Launay, David; Sobanski, Vincent; Dussart, Patricia; Chafey, Philippe; Broussard, Cédric; Duban-Deweer, Sophie; Vermersch, Patrick; Prin, Lionel; Lefranc, Didier
2015-01-01
Serological proteome analysis (SERPA) combines classical proteomic technology with effective separation of cellular protein extracts on two-dimensional gel electrophoresis, western blotting, and identification of the antigenic spot of interest by mass spectrometry. A critical point is related to the antigenic target characterization by mass spectrometry, which depends on the accuracy of the matching of antigenic reactivities on the protein spots during the 2D immunoproteomic procedures. The superimposition, based essentially on visual criteria of antigenic and protein spots, remains the major limitation of SERPA. The introduction of fluorescent dyes in proteomic strategies, commonly known as 2D-DIGE (differential in-gel electrophoresis), has boosted the qualitative capabilities of 2D electrophoresis. Based on this 2D-DIGE strategy, we have improved the conventional SERPA by developing a new and entirely fluorescence-based bi-dimensional immunoproteomic (FBIP) analysis, performed with three fluorescent dyes. To optimize the alignment of the different antigenic maps, we introduced a landmark map composed of a combination of specific antibodies. This methodological development allows simultaneous revelation of the antigenic, landmark and proteomic maps on each immunoblot. A computer-assisted process using commercially available software automatically leads to the superimposition of the different maps, ensuring accurate localization of antigenic spots of interest. PMID:26132557
Sun, Y. Y.; Kim, Y. H.; Lee, K.; Zhang, S. B.
2008-01-01
Density functional theory (DFT) in the commonly used local density or generalized gradient approximation fails to describe van der Waals (vdW) interactions that are vital to organic, biological, and other molecular systems. Here, we propose a simple, efficient, yet accurate local atomic potential (LAP) approach, named DFT+LAP, for including vdW interactions in the framework of DFT. The LAPs for H, C, N, and O are generated by fitting the DFT+LAP potential energy curves of small molecule dimers to those obtained from coupled cluster calculations with single, double, and perturbatively treated triple excitations, CCSD(T). Excellent transferability of the LAPs is demonstrated by remarkable agreement with the JSCH-2005 benchmark database [P. Jurecka et al. Phys. Chem. Chem. Phys. 8, 1985 (2006)], which provides the interaction energies of CCSD(T) quality for 165 vdW and hydrogen-bonded complexes. For over 100 vdW dominant complexes in this database, our DFT+LAP calculations give a mean absolute deviation from the benchmark results less than 0.5 kcal/mol. The DFT+LAP approach involves no extra computational cost other than standard DFT calculations and no modification of existing DFT codes, which enables straightforward quantum simulations, such as ab initio molecular dynamics, on biomolecular systems, as well as on other organic systems.
Computer Forensics Education - the Open Source Approach
NASA Astrophysics Data System (ADS)
Huebner, Ewa; Bem, Derek; Cheung, Hon
In this chapter we discuss the application of the open source software tools in computer forensics education at tertiary level. We argue that open source tools are more suitable than commercial tools, as they provide the opportunity for students to gain in-depth understanding and appreciation of the computer forensic process as opposed to familiarity with one software product, however complex and multi-functional. With the access to all source programs the students become more than just the consumers of the tools as future forensic investigators. They can also examine the code, understand the relationship between the binary images and relevant data structures, and in the process gain necessary background to become the future creators of new and improved forensic software tools. As a case study we present an advanced subject, Computer Forensics Workshop, which we designed for the Bachelor's degree in computer science at the University of Western Sydney. We based all laboratory work and the main take-home project in this subject on open source software tools. We found that without exception more than one suitable tool can be found to cover each topic in the curriculum adequately. We argue that this approach prepares students better for forensic field work, as they gain confidence to use a variety of tools, not just a single product they are familiar with.
Computational Approaches for Predicting Biomedical Research Collaborations
Zhang, Qing; Yu, Hong
2014-01-01
Biomedical research is increasingly collaborative, and successful collaborations often produce high impact work. Computational approaches can be developed for automatically predicting biomedical research collaborations. Previous works of collaboration prediction mainly explored the topological structures of research collaboration networks, leaving out rich semantic information from the publications themselves. In this paper, we propose supervised machine learning approaches to predict research collaborations in the biomedical field. We explored both the semantic features extracted from author research interest profile and the author network topological features. We found that the most informative semantic features for author collaborations are related to research interest, including similarity of out-citing citations, similarity of abstracts. Of the four supervised machine learning models (naïve Bayes, naïve Bayes multinomial, SVMs, and logistic regression), the best performing model is logistic regression with an ROC ranging from 0.766 to 0.980 on different datasets. To our knowledge we are the first to study in depth how research interest and productivities can be used for collaboration prediction. Our approach is computationally efficient, scalable and yet simple to implement. The datasets of this study are available at https://github.com/qingzhanggithub/medline-collaboration-datasets. PMID:25375164
A fourth order accurate finite difference scheme for the computation of elastic waves
NASA Technical Reports Server (NTRS)
Bayliss, A.; Jordan, K. E.; Lemesurier, B. J.; Turkel, E.
1986-01-01
A finite difference for elastic waves is introduced. The model is based on the first order system of equations for the velocities and stresses. The differencing is fourth order accurate on the spatial derivatives and second order accurate in time. The model is tested on a series of examples including the Lamb problem, scattering from plane interf aces and scattering from a fluid-elastic interface. The scheme is shown to be effective for these problems. The accuracy and stability is insensitive to the Poisson ratio. For the class of problems considered here it is found that the fourth order scheme requires for two-thirds to one-half the resolution of a typical second order scheme to give comparable accuracy.
A computational language approach to modeling prose recall in schizophrenia
Rosenstein, Mark; Diaz-Asper, Catherine; Foltz, Peter W.; Elvevåg, Brita
2014-01-01
Many cortical disorders are associated with memory problems. In schizophrenia, verbal memory deficits are a hallmark feature. However, the exact nature of this deficit remains elusive. Modeling aspects of language features used in memory recall have the potential to provide means for measuring these verbal processes. We employ computational language approaches to assess time-varying semantic and sequential properties of prose recall at various retrieval intervals (immediate, 30 min and 24 h later) in patients with schizophrenia, unaffected siblings and healthy unrelated control participants. First, we model the recall data to quantify the degradation of performance with increasing retrieval interval and the effect of diagnosis (i.e., group membership) on performance. Next we model the human scoring of recall performance using an n-gram language sequence technique, and then with a semantic feature based on Latent Semantic Analysis. These models show that automated analyses of the recalls can produce scores that accurately mimic human scoring. The final analysis addresses the validity of this approach by ascertaining the ability to predict group membership from models built on the two classes of language features. Taken individually, the semantic feature is most predictive, while a model combining the features improves accuracy of group membership prediction slightly above the semantic feature alone as well as over the human rating approach. We discuss the implications for cognitive neuroscience of such a computational approach in exploring the mechanisms of prose recall. PMID:24709122
A computational language approach to modeling prose recall in schizophrenia.
Rosenstein, Mark; Diaz-Asper, Catherine; Foltz, Peter W; Elvevåg, Brita
2014-06-01
Many cortical disorders are associated with memory problems. In schizophrenia, verbal memory deficits are a hallmark feature. However, the exact nature of this deficit remains elusive. Modeling aspects of language features used in memory recall have the potential to provide means for measuring these verbal processes. We employ computational language approaches to assess time-varying semantic and sequential properties of prose recall at various retrieval intervals (immediate, 30 min and 24 h later) in patients with schizophrenia, unaffected siblings and healthy unrelated control participants. First, we model the recall data to quantify the degradation of performance with increasing retrieval interval and the effect of diagnosis (i.e., group membership) on performance. Next we model the human scoring of recall performance using an n-gram language sequence technique, and then with a semantic feature based on Latent Semantic Analysis. These models show that automated analyses of the recalls can produce scores that accurately mimic human scoring. The final analysis addresses the validity of this approach by ascertaining the ability to predict group membership from models built on the two classes of language features. Taken individually, the semantic feature is most predictive, while a model combining the features improves accuracy of group membership prediction slightly above the semantic feature alone as well as over the human rating approach. We discuss the implications for cognitive neuroscience of such a computational approach in exploring the mechanisms of prose recall.
NASA Technical Reports Server (NTRS)
Goodwin, Sabine A.; Raj, P.
1999-01-01
Progress to date towards the development and validation of a fast, accurate and cost-effective aeroelastic method for advanced parallel computing platforms such as the IBM SP2 and the SGI Origin 2000 is presented in this paper. The ENSAERO code, developed at the NASA-Ames Research Center has been selected for this effort. The code allows for the computation of aeroelastic responses by simultaneously integrating the Euler or Navier-Stokes equations and the modal structural equations of motion. To assess the computational performance and accuracy of the ENSAERO code, this paper reports the results of the Navier-Stokes simulations of the transonic flow over a flexible aeroelastic wing body configuration. In addition, a forced harmonic oscillation analysis in the frequency domain and an analysis in the time domain are done on a wing undergoing a rigid pitch and plunge motion. Finally, to demonstrate the ENSAERO flutter-analysis capability, aeroelastic Euler and Navier-Stokes computations on an L-1011 wind tunnel model including pylon, nacelle and empennage are underway. All computational solutions are compared with experimental data to assess the level of accuracy of ENSAERO. As the computations described above are performed, a meticulous log of computational performance in terms of wall clock time, execution speed, memory and disk storage is kept. Code scalability is also demonstrated by studying the impact of varying the number of processors on computational performance on the IBM SP2 and the Origin 2000 systems.
NASA Astrophysics Data System (ADS)
Ng, C. N.; Chu, T. P.; Wu, Huasheng; Tong, S. Y.; Huang, Hong
1997-03-01
We compare multiple scattering results of angle-resolved photoelectron diffraction spectra between the exact slab method and the separable propagator perturbation method. In the slab method,footnote C.H. Li, A.R. Lubinsky and S.Y. Tong, Phys. Rev. B17, 3128 (1978). the source wave and multiple scattering within the strong scattering atomic layers are expanded in spherical waves while interlayer scattering is expressed in plane waves. The transformation between spherical waves and plane waves is done exactly. The plane waves are then matched across the solid-vacuum interface to a single outgoing plane wave in the detector's direction. The separable propagator perturbation approach uses two approximations: (i) A separable representation of the Green's function propagator and (ii) A perturbation expansion of multiple scattering terms. Results of c(2x2) S-Ni(001) show that this approximate method fails to converge due to the very slow convergence of the separable representation for scattering angles less than 90^circ. However, this method is accurate in the backscattering regime and may be applied to XAFS calculations.(J.J. Rehr and R.C. Albers, Phys. Rev. B41, 8139 (1990).) The use of this method for angle-resolved photoelectron diffraction spectra is substantially less reliable.
Sculpting the band gap: a computational approach.
Prasai, Kiran; Biswas, Parthapratim; Drabold, D A
2015-01-01
Materials with optimized band gap are needed in many specialized applications. In this work, we demonstrate that Hellmann-Feynman forces associated with the gap states can be used to find atomic coordinates that yield desired electronic density of states. Using tight-binding models, we show that this approach may be used to arrive at electronically designed models of amorphous silicon and carbon. We provide a simple recipe to include a priori electronic information in the formation of computer models of materials, and prove that this information may have profound structural consequences. The models are validated with plane-wave density functional calculations. PMID:26490203
Varghese, Bino; Short, David; Penmetsa, Ravi; Goswami, Tarun; Hangartner, Thomas
2011-04-29
Finite element (FE) models of long bones constructed from computed-tomography (CT) data are emerging as an invaluable tool in the field of bone biomechanics. However, the performance of such FE models is highly dependent on the accurate capture of geometry and appropriate assignment of material properties. In this study, a combined numerical-experimental study is performed comparing FE-predicted surface strains with strain-gauge measurements. Thirty-six major, cadaveric, long bones (humerus, radius, femur and tibia), which cover a wide range of bone sizes, were tested under three-point bending and torsion. The FE models were constructed from trans-axial volumetric CT scans, and the segmented bone images were corrected for partial-volume effects. The material properties (Young's modulus for cortex, density-modulus relationship for trabecular bone and Poisson's ratio) were calibrated by minimizing the error between experiments and simulations among all bones. The R(2) values of the measured strains versus load under three-point bending and torsion were 0.96-0.99 and 0.61-0.99, respectively, for all bones in our dataset. The errors of the calculated FE strains in comparison to those measured using strain gauges in the mechanical tests ranged from -6% to 7% under bending and from -37% to 19% under torsion. The observation of comparatively low errors and high correlations between the FE-predicted strains and the experimental strains, across the various types of bones and loading conditions (bending and torsion), validates our approach to bone segmentation and our choice of material properties.
Time-Accurate Computations of Isolated Circular Synthetic Jets in Crossflow
NASA Technical Reports Server (NTRS)
Rumsey, C. L.; Schaeffler, N. W.; Milanovic, I. M.; Zaman, K. B. M. Q.
2007-01-01
Results from unsteady Reynolds-averaged Navier-Stokes computations are described for two different synthetic jet flows issuing into a turbulent boundary layer crossflow through a circular orifice. In one case the jet effect is mostly contained within the boundary layer, while in the other case the jet effect extends beyond the boundary layer edge. Both cases have momentum flux ratios less than 2. Several numerical parameters are investigated, and some lessons learned regarding the CFD methods for computing these types of flow fields are summarized. Results in both cases are compared to experiment.
Time-Accurate Computations of Isolated Circular Synthetic Jets in Crossflow
NASA Technical Reports Server (NTRS)
Rumsey, Christoper L.; Schaeffler, Norman W.; Milanovic, I. M.; Zaman, K. B. M. Q.
2005-01-01
Results from unsteady Reynolds-averaged Navier-Stokes computations are described for two different synthetic jet flows issuing into a turbulent boundary layer crossflow through a circular orifice. In one case the jet effect is mostly contained within the boundary layer, while in the other case the jet effect extends beyond the boundary layer edge. Both cases have momentum flux ratios less than 2. Several numerical parameters are investigated, and some lessons learned regarding the CFD methods for computing these types of flow fields are outlined. Results in both cases are compared to experiment.
Computer subroutine ISUDS accurately solves large system of simultaneous linear algebraic equations
NASA Technical Reports Server (NTRS)
Collier, G.
1967-01-01
Computer program, an Iterative Scheme Using a Direct Solution, obtains double precision accuracy using a single-precision coefficient matrix. ISUDS solves a system of equations written in matrix form as AX equals B, where A is a square non-singular coefficient matrix, X is a vector, and B is a vector.
Computational approaches to motor learning by imitation.
Schaal, Stefan; Ijspeert, Auke; Billard, Aude
2003-01-01
Movement imitation requires a complex set of mechanisms that map an observed movement of a teacher onto one's own movement apparatus. Relevant problems include movement recognition, pose estimation, pose tracking, body correspondence, coordinate transformation from external to egocentric space, matching of observed against previously learned movement, resolution of redundant degrees-of-freedom that are unconstrained by the observation, suitable movement representations for imitation, modularization of motor control, etc. All of these topics by themselves are active research problems in computational and neurobiological sciences, such that their combination into a complete imitation system remains a daunting undertaking-indeed, one could argue that we need to understand the complete perception-action loop. As a strategy to untangle the complexity of imitation, this paper will examine imitation purely from a computational point of view, i.e. we will review statistical and mathematical approaches that have been suggested for tackling parts of the imitation problem, and discuss their merits, disadvantages and underlying principles. Given the focus on action recognition of other contributions in this special issue, this paper will primarily emphasize the motor side of imitation, assuming that a perceptual system has already identified important features of a demonstrated movement and created their corresponding spatial information. Based on the formalization of motor control in terms of control policies and their associated performance criteria, useful taxonomies of imitation learning can be generated that clarify different approaches and future research directions. PMID:12689379
Matrix-vector multiplication using digital partitioning for more accurate optical computing
NASA Technical Reports Server (NTRS)
Gary, C. K.
1992-01-01
Digital partitioning offers a flexible means of increasing the accuracy of an optical matrix-vector processor. This algorithm can be implemented with the same architecture required for a purely analog processor, which gives optical matrix-vector processors the ability to perform high-accuracy calculations at speeds comparable with or greater than electronic computers as well as the ability to perform analog operations at a much greater speed. Digital partitioning is compared with digital multiplication by analog convolution, residue number systems, and redundant number representation in terms of the size and the speed required for an equivalent throughput as well as in terms of the hardware requirements. Digital partitioning and digital multiplication by analog convolution are found to be the most efficient alogrithms if coding time and hardware are considered, and the architecture for digital partitioning permits the use of analog computations to provide the greatest throughput for a single processor.
NASA Technical Reports Server (NTRS)
Ellison, Donald; Conway, Bruce; Englander, Jacob
2015-01-01
A significant body of work exists showing that providing a nonlinear programming (NLP) solver with expressions for the problem constraint gradient substantially increases the speed of program execution and can also improve the robustness of convergence, especially for local optimizers. Calculation of these derivatives is often accomplished through the computation of spacecraft's state transition matrix (STM). If the two-body gravitational model is employed as is often done in the context of preliminary design, closed form expressions for these derivatives may be provided. If a high fidelity dynamics model, that might include perturbing forces such as the gravitational effect from multiple third bodies and solar radiation pressure is used then these STM's must be computed numerically. We present a method for the power hardward model and a full ephemeris model. An adaptive-step embedded eight order Dormand-Prince numerical integrator is discussed and a method for the computation of the time of flight derivatives in this framework is presented. The use of these numerically calculated derivatieves offer a substantial improvement over finite differencing in the context of a global optimizer. Specifically the inclusion of these STM's into the low thrust missiondesign tool chain in use at NASA Goddard Spaceflight Center allows for an increased preliminary mission design cadence.
NASA Technical Reports Server (NTRS)
Vaughan, William W.; Friedman, Mark J.; Monteiro, Anand C.
1993-01-01
In earlier papers, Doedel and the authors have developed a numerical method and derived error estimates for the computation of branches of heteroclinic orbits for a system of autonomous ordinary differential equations in R(exp n). The idea of the method is to reduce a boundary value problem on the real line to a boundary value problem on a finite interval by using a local (linear or higher order) approximation of the stable and unstable manifolds. A practical limitation for the computation of homoclinic and heteroclinic orbits has been the difficulty in obtaining starting orbits. Typically these were obtained from a closed form solution or via a homotopy from a known solution. Here we consider extensions of our algorithm which allow us to obtain starting orbits on the continuation branch in a more systematic way as well as make the continuation algorithm more flexible. In applications, we use the continuation software package AUTO in combination with some initial value software. The examples considered include computation of homoclinic orbits in a singular perturbation problem and in a turbulent fluid boundary layer in the wall region problem.
Johnson, K.A.; Holman, B.L.; Rosen, T.J.; Nagel, J.S.; English, R.J.; Growdon, J.H. )
1990-04-01
To determine the diagnostic accuracy of iofetamine hydrochloride I 123 (IMP) with single photon emission computed tomography in Alzheimer's disease, we studied 58 patients with AD and 15 age-matched healthy control subjects. We used a qualitative method to assess regional IMP uptake in the entire brain and to rate image data sets as normal or abnormal without knowledge of subjects'clinical classification. The sensitivity and specificity of IMP with single photon emission computed tomography in AD were 88% and 87%, respectively. In 15 patients with mild cognitive deficits (Blessed Dementia Scale score, less than or equal to 10), sensitivity was 80%. With the use of a semiquantitative measure of regional cortical IMP uptake, the parietal lobes were the most functionally impaired in AD and the most strongly associated with the patients' Blessed Dementia Scale scores. These results indicated that IMP with single photon emission computed tomography may be a useful adjunct in the clinical diagnosis of AD in early, mild disease.
A mechanistic approach for accurate simulation of village scale malaria transmission
Bomblies, Arne; Duchemin, Jean-Bernard; Eltahir, Elfatih AB
2009-01-01
Background Malaria transmission models commonly incorporate spatial environmental and climate variability for making regional predictions of disease risk. However, a mismatch of these models' typical spatial resolutions and the characteristic scale of malaria vector population dynamics may confound disease risk predictions in areas of high spatial hydrological variability such as the Sahel region of Africa. Methods Field observations spanning two years from two Niger villages are compared. The two villages are separated by only 30 km but exhibit a ten-fold difference in anopheles mosquito density. These two villages would be covered by a single grid cell in many malaria models, yet their entomological activity differs greatly. Environmental conditions and associated entomological activity are simulated at high spatial- and temporal resolution using a mechanistic approach that couples a distributed hydrology scheme and an entomological model. Model results are compared to regular field observations of Anopheles gambiae sensu lato mosquito populations and local hydrology. The model resolves the formation and persistence of individual pools that facilitate mosquito breeding and predicts spatio-temporal mosquito population variability at high resolution using an agent-based modeling approach. Results Observations of soil moisture, pool size, and pool persistence are reproduced by the model. The resulting breeding of mosquitoes in the simulated pools yields time-integrated seasonal mosquito population dynamics that closely follow observations from captured mosquito abundance. Interannual difference in mosquito abundance is simulated, and the inter-village difference in mosquito population is reproduced for two years of observations. These modeling results emulate the known focal nature of malaria in Niger Sahel villages. Conclusion Hydrological variability must be represented at high spatial and temporal resolution to achieve accurate predictive ability of malaria risk
Osei-Kuffuor, Daniel; Fattebert, Jean-Luc
2014-01-01
We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101 952 atoms on 23 328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7x10^{-4} Ha/Bohr.
NASA Astrophysics Data System (ADS)
Alexandre, E.; Cuadra, L.; Nieto-Borge, J. C.; Candil-García, G.; del Pino, M.; Salcedo-Sanz, S.
2015-08-01
Wave parameters computed from time series measured by buoys (significant wave height Hs, mean wave period, etc.) play a key role in coastal engineering and in the design and operation of wave energy converters. Storms or navigation accidents can make measuring buoys break down, leading to missing data gaps. In this paper we tackle the problem of locally reconstructing Hs at out-of-operation buoys by using wave parameters from nearby buoys, based on the spatial correlation among values at neighboring buoy locations. The novelty of our approach for its potential application to problems in coastal engineering is twofold. On one hand, we propose a genetic algorithm hybridized with an extreme learning machine that selects, among the available wave parameters from the nearby buoys, a subset FnSP with nSP parameters that minimizes the Hs reconstruction error. On the other hand, we evaluate to what extent the selected parameters in subset FnSP are good enough in assisting other machine learning (ML) regressors (extreme learning machines, support vector machines and gaussian process regression) to reconstruct Hs. The results show that all the ML method explored achieve a good Hs reconstruction in the two different locations studied (Caribbean Sea and West Atlantic).
An adaptive grid method for computing time accurate solutions on structured grids
NASA Technical Reports Server (NTRS)
Bockelie, Michael J.; Smith, Robert E.; Eiseman, Peter R.
1991-01-01
The solution method consists of three parts: a grid movement scheme; an unsteady Euler equation solver; and a temporal coupling routine that links the dynamic grid to the Euler solver. The grid movement scheme is an algebraic method containing grid controls that generate a smooth grid that resolves the severe solution gradients and the sharp transitions in the solution gradients. The temporal coupling is performed with a grid prediction correction procedure that is simple to implement and provides a grid that does not lag the solution in time. The adaptive solution method is tested by computing the unsteady inviscid solutions for a one dimensional shock tube and a two dimensional shock vortex iteraction.
Gravitational Focusing and the Computation of an Accurate Moon/Mars Cratering Ratio
NASA Technical Reports Server (NTRS)
Matney, Mark J.
2006-01-01
There have been a number of attempts to use asteroid populations to simultaneously compute cratering rates on the Moon and bodies elsewhere in the Solar System to establish the cratering ratio (e.g., [1],[2]). These works use current asteroid orbit population databases combined with collision rate calculations based on orbit intersections alone. As recent work on meteoroid fluxes [3] have highlighted, however, collision rates alone are insufficient to describe the cratering rates on planetary surfaces - especially planets with stronger gravitational fields than the Moon, such as Earth and Mars. Such calculations also need to include the effects of gravitational focusing, whereby the spatial density of the slower-moving impactors is preferentially "focused" by the gravity of the body. This leads overall to higher fluxes and cratering rates, and is highly dependent on the detailed velocity distributions of the impactors. In this paper, a comprehensive gravitational focusing algorithm originally developed to describe fluxes of interplanetary meteoroids [3] is applied to the collision rates and cratering rates of populations of asteroids and long-period comets to compute better cratering ratios for terrestrial bodies in the Solar System. These results are compared to the calculations of other researchers.
NASA Astrophysics Data System (ADS)
Kees, C. E.; Farthing, M. W.; Terrel, A.; Certik, O.; Seljebotn, D.
2013-12-01
This presentation will focus on two barriers to progress in the hydrological modeling community, and research and development conducted to lessen or eliminate them. The first is a barrier to sharing hydrological models among specialized scientists that is caused by intertwining the implementation of numerical methods with the implementation of abstract numerical modeling information. In the Proteus toolkit for computational methods and simulation, we have decoupled these two important parts of computational model through separate "physics" and "numerics" interfaces. More recently we have begun developing the Strong Form Language for easy and direct representation of the mathematical model formulation in a domain specific language embedded in Python. The second major barrier is sharing ANY scientific software tools that have complex library or module dependencies, as most parallel, multi-physics hydrological models must have. In this setting, users and developer are dependent on an entire distribution, possibly depending on multiple compilers and special instructions depending on the environment of the target machine. To solve these problem we have developed, hashdist, a stateless package management tool and a resulting portable, open source scientific software distribution.
A computational approach to negative priming
NASA Astrophysics Data System (ADS)
Schrobsdorff, H.; Ihrke, M.; Kabisch, B.; Behrendt, J.; Hasselhorn, M.; Herrmann, J. Michael
2007-09-01
Priming is characterized by a sensitivity of reaction times to the sequence of stimuli in psychophysical experiments. The reduction of the reaction time observed in positive priming is well-known and experimentally understood (Scarborough et al., J. Exp. Psycholol: Hum. Percept. Perform., 3, pp. 1-17, 1977). Negative priming—the opposite effect—is experimentally less tangible (Fox, Psychonom. Bull. Rev., 2, pp. 145-173, 1995). The dependence on subtle parameter changes (such as response-stimulus interval) usually varies. The sensitivity of the negative priming effect bears great potential for applications in research in fields such as memory, selective attention, and ageing effects. We develop and analyse a computational realization, CISAM, of a recent psychological model for action decision making, the ISAM (Kabisch, PhD thesis, Friedrich-Schiller-Universitat, 2003), which is sensitive to priming conditions. With the dynamical systems approach of the CISAM, we show that a single adaptive threshold mechanism is sufficient to explain both positive and negative priming effects. This is achieved by comparing results obtained by the computational modelling with experimental data from our laboratory. The implementation provides a rich base from which testable predictions can be derived, e.g. with respect to hitherto untested stimulus combinations (e.g. single-object trials).
Fast and accurate CMB computations in non-flat FLRW universes
Lesgourgues, Julien; Tram, Thomas E-mail: thomas.tram@epfl.ch
2014-09-01
We present a new method for calculating CMB anisotropies in a non-flat Friedmann universe, relying on a very stable algorithm for the calculation of hyperspherical Bessel functions, that can be pushed to arbitrary precision levels. We also introduce a new approximation scheme which gradually takes over in the flat space limit and leads to significant reductions of the computation time. Our method is implemented in the Boltzmann code class. It can be used to benchmark the accuracy of the camb code in curved space, which is found to match expectations. For default precision settings, corresponding to 0.1% for scalar temperature spectra and 0.2% for scalar polarisation spectra, our code is two to three times faster, depending on curvature. We also simplify the temperature and polarisation source terms significantly, so the different contributions to the C{sub ℓ} 's are easy to identify inside the code.
NASA Technical Reports Server (NTRS)
Kemp, James Herbert (Inventor); Talukder, Ashit (Inventor); Lambert, James (Inventor); Lam, Raymond (Inventor)
2008-01-01
A computer-implemented system and method of intra-oral analysis for measuring plaque removal is disclosed. The system includes hardware for real-time image acquisition and software to store the acquired images on a patient-by-patient basis. The system implements algorithms to segment teeth of interest from surrounding gum, and uses a real-time image-based morphing procedure to automatically overlay a grid onto each segmented tooth. Pattern recognition methods are used to classify plaque from surrounding gum and enamel, while ignoring glare effects due to the reflection of camera light and ambient light from enamel regions. The system integrates these components into a single software suite with an easy-to-use graphical user interface (GUI) that allows users to do an end-to-end run of a patient record, including tooth segmentation of all teeth, grid morphing of each segmented tooth, and plaque classification of each tooth image.
A model for the accurate computation of the lateral scattering of protons in water.
Bellinzona, E V; Ciocca, M; Embriaco, A; Ferrari, A; Fontana, A; Mairani, A; Parodi, K; Rotondi, A; Sala, P; Tessonnier, T
2016-02-21
A pencil beam model for the calculation of the lateral scattering in water of protons for any therapeutic energy and depth is presented. It is based on the full Molière theory, taking into account the energy loss and the effects of mixtures and compounds. Concerning the electromagnetic part, the model has no free parameters and is in very good agreement with the FLUKA Monte Carlo (MC) code. The effects of the nuclear interactions are parametrized with a two-parameter tail function, adjusted on MC data calculated with FLUKA. The model, after the convolution with the beam and the detector response, is in agreement with recent proton data in water from HIT. The model gives results with the same accuracy of the MC codes based on Molière theory, with a much shorter computing time.
A model for the accurate computation of the lateral scattering of protons in water
NASA Astrophysics Data System (ADS)
Bellinzona, E. V.; Ciocca, M.; Embriaco, A.; Ferrari, A.; Fontana, A.; Mairani, A.; Parodi, K.; Rotondi, A.; Sala, P.; Tessonnier, T.
2016-02-01
A pencil beam model for the calculation of the lateral scattering in water of protons for any therapeutic energy and depth is presented. It is based on the full Molière theory, taking into account the energy loss and the effects of mixtures and compounds. Concerning the electromagnetic part, the model has no free parameters and is in very good agreement with the FLUKA Monte Carlo (MC) code. The effects of the nuclear interactions are parametrized with a two-parameter tail function, adjusted on MC data calculated with FLUKA. The model, after the convolution with the beam and the detector response, is in agreement with recent proton data in water from HIT. The model gives results with the same accuracy of the MC codes based on Molière theory, with a much shorter computing time.
Quick, Accurate, Smart: 3D Computer Vision Technology Helps Assessing Confined Animals’ Behaviour
Calderara, Simone; Pistocchi, Simone; Cucchiara, Rita; Podaliri-Vulpiani, Michele; Messori, Stefano; Ferri, Nicola
2016-01-01
Mankind directly controls the environment and lifestyles of several domestic species for purposes ranging from production and research to conservation and companionship. These environments and lifestyles may not offer these animals the best quality of life. Behaviour is a direct reflection of how the animal is coping with its environment. Behavioural indicators are thus among the preferred parameters to assess welfare. However, behavioural recording (usually from video) can be very time consuming and the accuracy and reliability of the output rely on the experience and background of the observers. The outburst of new video technology and computer image processing gives the basis for promising solutions. In this pilot study, we present a new prototype software able to automatically infer the behaviour of dogs housed in kennels from 3D visual data and through structured machine learning frameworks. Depth information acquired through 3D features, body part detection and training are the key elements that allow the machine to recognise postures, trajectories inside the kennel and patterns of movement that can be later labelled at convenience. The main innovation of the software is its ability to automatically cluster frequently observed temporal patterns of movement without any pre-set ethogram. Conversely, when common patterns are defined through training, a deviation from normal behaviour in time or between individuals could be assessed. The software accuracy in correctly detecting the dogs’ behaviour was checked through a validation process. An automatic behaviour recognition system, independent from human subjectivity, could add scientific knowledge on animals’ quality of life in confinement as well as saving time and resources. This 3D framework was designed to be invariant to the dog’s shape and size and could be extended to farm, laboratory and zoo quadrupeds in artificial housing. The computer vision technique applied to this software is innovative in non
Quick, Accurate, Smart: 3D Computer Vision Technology Helps Assessing Confined Animals' Behaviour.
Barnard, Shanis; Calderara, Simone; Pistocchi, Simone; Cucchiara, Rita; Podaliri-Vulpiani, Michele; Messori, Stefano; Ferri, Nicola
2016-01-01
Mankind directly controls the environment and lifestyles of several domestic species for purposes ranging from production and research to conservation and companionship. These environments and lifestyles may not offer these animals the best quality of life. Behaviour is a direct reflection of how the animal is coping with its environment. Behavioural indicators are thus among the preferred parameters to assess welfare. However, behavioural recording (usually from video) can be very time consuming and the accuracy and reliability of the output rely on the experience and background of the observers. The outburst of new video technology and computer image processing gives the basis for promising solutions. In this pilot study, we present a new prototype software able to automatically infer the behaviour of dogs housed in kennels from 3D visual data and through structured machine learning frameworks. Depth information acquired through 3D features, body part detection and training are the key elements that allow the machine to recognise postures, trajectories inside the kennel and patterns of movement that can be later labelled at convenience. The main innovation of the software is its ability to automatically cluster frequently observed temporal patterns of movement without any pre-set ethogram. Conversely, when common patterns are defined through training, a deviation from normal behaviour in time or between individuals could be assessed. The software accuracy in correctly detecting the dogs' behaviour was checked through a validation process. An automatic behaviour recognition system, independent from human subjectivity, could add scientific knowledge on animals' quality of life in confinement as well as saving time and resources. This 3D framework was designed to be invariant to the dog's shape and size and could be extended to farm, laboratory and zoo quadrupeds in artificial housing. The computer vision technique applied to this software is innovative in non
Quick, Accurate, Smart: 3D Computer Vision Technology Helps Assessing Confined Animals' Behaviour.
Barnard, Shanis; Calderara, Simone; Pistocchi, Simone; Cucchiara, Rita; Podaliri-Vulpiani, Michele; Messori, Stefano; Ferri, Nicola
2016-01-01
Mankind directly controls the environment and lifestyles of several domestic species for purposes ranging from production and research to conservation and companionship. These environments and lifestyles may not offer these animals the best quality of life. Behaviour is a direct reflection of how the animal is coping with its environment. Behavioural indicators are thus among the preferred parameters to assess welfare. However, behavioural recording (usually from video) can be very time consuming and the accuracy and reliability of the output rely on the experience and background of the observers. The outburst of new video technology and computer image processing gives the basis for promising solutions. In this pilot study, we present a new prototype software able to automatically infer the behaviour of dogs housed in kennels from 3D visual data and through structured machine learning frameworks. Depth information acquired through 3D features, body part detection and training are the key elements that allow the machine to recognise postures, trajectories inside the kennel and patterns of movement that can be later labelled at convenience. The main innovation of the software is its ability to automatically cluster frequently observed temporal patterns of movement without any pre-set ethogram. Conversely, when common patterns are defined through training, a deviation from normal behaviour in time or between individuals could be assessed. The software accuracy in correctly detecting the dogs' behaviour was checked through a validation process. An automatic behaviour recognition system, independent from human subjectivity, could add scientific knowledge on animals' quality of life in confinement as well as saving time and resources. This 3D framework was designed to be invariant to the dog's shape and size and could be extended to farm, laboratory and zoo quadrupeds in artificial housing. The computer vision technique applied to this software is innovative in non
Time-Accurate Computational Fluid Dynamics Simulation of a Pair of Moving Solid Rocket Boosters
NASA Technical Reports Server (NTRS)
Strutzenberg, Louise L.; Williams, Brandon R.
2011-01-01
Since the Columbia accident, the threat to the Shuttle launch vehicle from debris during the liftoff timeframe has been assessed by the Liftoff Debris Team at NASA/MSFC. In addition to engineering methods of analysis, CFD-generated flow fields during the liftoff timeframe have been used in conjunction with 3-DOF debris transport methods to predict the motion of liftoff debris. Early models made use of a quasi-steady flow field approximation with the vehicle positioned at a fixed location relative to the ground; however, a moving overset mesh capability has recently been developed for the Loci/CHEM CFD software which enables higher-fidelity simulation of the Shuttle transient plume startup and liftoff environment. The present work details the simulation of the launch pad and mobile launch platform (MLP) with truncated solid rocket boosters (SRBs) moving in a prescribed liftoff trajectory derived from Shuttle flight measurements. Using Loci/CHEM, time-accurate RANS and hybrid RANS/LES simulations were performed for the timeframe T0+0 to T0+3.5 seconds, which consists of SRB startup to a vehicle altitude of approximately 90 feet above the MLP. Analysis of the transient flowfield focuses on the evolution of the SRB plumes in the MLP plume holes and the flame trench, impingement on the flame deflector, and especially impingment on the MLP deck resulting in upward flow which is a transport mechanism for debris. The results show excellent qualitative agreement with the visual record from past Shuttle flights, and comparisons to pressure measurements in the flame trench and on the MLP provide confidence in these simulation capabilities.
NASA Astrophysics Data System (ADS)
Osei-Kuffuor, Daniel; Fattebert, Jean-Luc
2014-03-01
We present a truly scalable First-Principles Molecular Dynamics algorithm with O(N) complexity and fully controllable accuracy, capable of simulating systems of sizes that were previously impossible with this degree of accuracy. By avoiding global communication, we have extended W. Kohn's condensed matter ``nearsightedness'' principle to a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wavefunctions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 100,000 atoms on 100,000 processors, with a wall-clock time of the order of one minute per molecular dynamics time step. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.
Computational approaches to predict bacteriophage-host relationships.
Edwards, Robert A; McNair, Katelyn; Faust, Karoline; Raes, Jeroen; Dutilh, Bas E
2016-03-01
Metagenomics has changed the face of virus discovery by enabling the accurate identification of viral genome sequences without requiring isolation of the viruses. As a result, metagenomic virus discovery leaves the first and most fundamental question about any novel virus unanswered: What host does the virus infect? The diversity of the global virosphere and the volumes of data obtained in metagenomic sequencing projects demand computational tools for virus-host prediction. We focus on bacteriophages (phages, viruses that infect bacteria), the most abundant and diverse group of viruses found in environmental metagenomes. By analyzing 820 phages with annotated hosts, we review and assess the predictive power of in silico phage-host signals. Sequence homology approaches are the most effective at identifying known phage-host pairs. Compositional and abundance-based methods contain significant signal for phage-host classification, providing opportunities for analyzing the unknowns in viral metagenomes. Together, these computational approaches further our knowledge of the interactions between phages and their hosts. Importantly, we find that all reviewed signals significantly link phages to their hosts, illustrating how current knowledge and insights about the interaction mechanisms and ecology of coevolving phages and bacteria can be exploited to predict phage-host relationships, with potential relevance for medical and industrial applications.
Highly Accurate Frequency Calculations of Crab Cavities Using the VORPAL Computational Framework
Austin, T.M.; Cary, J.R.; Bellantoni, L.; /Argonne
2009-05-01
We have applied the Werner-Cary method [J. Comp. Phys. 227, 5200-5214 (2008)] for extracting modes and mode frequencies from time-domain simulations of crab cavities, as are needed for the ILC and the beam delivery system of the LHC. This method for frequency extraction relies on a small number of simulations, and post-processing using the SVD algorithm with Tikhonov regularization. The time-domain simulations were carried out using the VORPAL computational framework, which is based on the eminently scalable finite-difference time-domain algorithm. A validation study was performed on an aluminum model of the 3.9 GHz RF separators built originally at Fermi National Accelerator Laboratory in the US. Comparisons with measurements of the A15 cavity show that this method can provide accuracy to within 0.01% of experimental results after accounting for manufacturing imperfections. To capture the near degeneracies two simulations, requiring in total a few hours on 600 processors were employed. This method has applications across many areas including obtaining MHD spectra from time-domain simulations.
Gray, Alan; Harlen, Oliver G.; Harris, Sarah A.; Khalid, Syma; Leung, Yuk Ming; Lonsdale, Richard; Mulholland, Adrian J.; Pearson, Arwen R.; Read, Daniel J.; Richardson, Robin A.
2015-01-01
Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational. PMID:25615870
Vela, Sergi; Fumanal, Maria; Ribas-Arino, Jordi; Robert, Vincent
2015-07-01
The DFT + U methodology is regarded as one of the most-promising strategies to treat the solid state of molecular materials, as it may provide good energetic accuracy at a moderate computational cost. However, a careful parametrization of the U-term is mandatory since the results may be dramatically affected by the selected value. Herein, we benchmarked the Hubbard-like U-term for seven Fe(ii)N6-based pseudo-octahedral spin crossover (SCO) compounds, using as a reference an estimation of the electronic enthalpy difference (ΔHelec) extracted from experimental data (T1/2, ΔS and ΔH). The parametrized U-value obtained for each of those seven compounds ranges from 2.37 eV to 2.97 eV, with an average value of U = 2.65 eV. Interestingly, we have found that this average value can be taken as a good starting point since it leads to an unprecedented mean absolute error (MAE) of only 4.3 kJ mol(-1) in the evaluation of ΔHelec for the studied compounds. Moreover, by comparing our results on the solid state and the gas phase of the materials, we quantify the influence of the intermolecular interactions on the relative stability of the HS and LS states, with an average effect of ca. 5 kJ mol(-1), whose sign cannot be generalized. Overall, the findings reported in this manuscript pave the way for future studies devoted to understand the crystalline phase of SCO compounds, or the adsorption of individual molecules on organic or metallic surfaces, in which the rational incorporation of the U-term within DFT + U yields the required energetic accuracy that is dramatically missing when using bare-DFT functionals.
Accurate micro-computed tomography imaging of pore spaces in collagen-based scaffold.
Zidek, Jan; Vojtova, Lucy; Abdel-Mohsen, A M; Chmelik, Jiri; Zikmund, Tomas; Brtnikova, Jana; Jakubicek, Roman; Zubal, Lukas; Jan, Jiri; Kaiser, Jozef
2016-06-01
In this work we have used X-ray micro-computed tomography (μCT) as a method to observe the morphology of 3D porous pure collagen and collagen-composite scaffolds useful in tissue engineering. Two aspects of visualizations were taken into consideration: improvement of the scan and investigation of its sensitivity to the scan parameters. Due to the low material density some parts of collagen scaffolds are invisible in a μCT scan. Therefore, here we present different contrast agents, which increase the contrast of the scanned biopolymeric sample for μCT visualization. The increase of contrast of collagenous scaffolds was performed with ceramic hydroxyapatite microparticles (HAp), silver ions (Ag(+)) and silver nanoparticles (Ag-NPs). Since a relatively small change in imaging parameters (e.g. in 3D volume rendering, threshold value and μCT acquisition conditions) leads to a completely different visualized pattern, we have optimized these parameters to obtain the most realistic picture for visual and qualitative evaluation of the biopolymeric scaffold. Moreover, scaffold images were stereoscopically visualized in order to better see the 3D biopolymer composite scaffold morphology. However, the optimized visualization has some discontinuities in zoomed view, which can be problematic for further analysis of interconnected pores by commonly used numerical methods. Therefore, we applied the locally adaptive method to solve discontinuities issue. The combination of contrast agent and imaging techniques presented in this paper help us to better understand the structure and morphology of the biopolymeric scaffold that is crucial in the design of new biomaterials useful in tissue engineering. PMID:27153826
NASA Astrophysics Data System (ADS)
Yi, Sha-Sha; Pan, Cong; Hu, Zhong-Han
2015-12-01
Modern computer simulations of biological systems often involve an explicit treatment of the complex interactions among a large number of molecules. While it is straightforward to compute the short-ranged Van der Waals interaction in classical molecular dynamics simulations, it has been a long-lasting issue to develop accurate methods for the longranged Coulomb interaction. In this short review, we discuss three types of methodologies for the accurate treatment of electrostatics in simulations of explicit molecules: truncation-type methods, Ewald-type methods, and mean-field-type methods. Throughout the discussion, we brief the formulations and developments of these methods, emphasize the intrinsic connections among the three types of methods, and focus on the existing problems which are often associated with the boundary conditions of electrostatics. This brief survey is summarized with a short perspective on future trends along the method developments and applications in the field of biological simulations. Project supported by the National Natural Science Foundation of China (Grant Nos. 91127015 and 21522304) and the Open Project from the State Key Laboratory of Theoretical Physics, and the Innovation Project from the State Key Laboratory of Supramolecular Structure and Materials.
Chavanon, O; Barbe, C; Troccaz, J; Carrat, L; Ribuot, C; Noirclerc, M; Maitrasse, B; Blin, D
1999-06-01
In the field of percutaneous access to soft tissues, our project was to improve classical pericardiocentesis by performing accurate guidance to a selected target, according to a model of the pericardial effusion acquired through three-dimensional (3D) data recording. Required hardware is an echocardiographic device and a needle, both linked to a 3D localizer, and a computer. After acquiring echographic data, a modeling procedure allows definition of the optimal puncture strategy, taking into consideration the mobility of the heart, by determining a stable region, whatever the period of the cardiac cycle. A passive guidance system is then used to reach the planned target accurately, generally a site in the middle of the stable region. After validation on a dynamic phantom and a feasibility study in dogs, an accuracy and reliability analysis protocol was realized on pigs with experimental pericardial effusion. Ten consecutive successful punctures using various trajectories were performed on eight pigs. Nonbloody liquid was collected from pericardial effusions in the stable region (5 to 9 mm wide) within 10 to 15 minutes from echographic acquisition to drainage. Accuracy of at least 2.5 mm was demonstrated. This study demonstrates the feasibility of computer-assisted pericardiocentesis. Beyond the simple improvement of the current technique, this method could be a new way to reach the heart or a new tool for percutaneous access and image-guided puncture of soft tissues. Further investigation will be necessary before routine human application.
Manz, Thomas A; Sholl, David S
2011-12-13
The partitioning of electron spin density among atoms in a material gives atomic spin moments (ASMs), which are important for understanding magnetic properties. We compare ASMs computed using different population analysis methods and introduce a method for computing density derived electrostatic and chemical (DDEC) ASMs. Bader and DDEC ASMs can be computed for periodic and nonperiodic materials with either collinear or noncollinear magnetism, while natural population analysis (NPA) ASMs can be computed for nonperiodic materials with collinear magnetism. Our results show Bader, DDEC, and (where applicable) NPA methods give similar ASMs, but different net atomic charges. Because they are optimized to reproduce both the magnetic field and the chemical states of atoms in a material, DDEC ASMs are especially suitable for constructing interaction potentials for atomistic simulations. We describe the computation of accurate ASMs for (a) a variety of systems using collinear and noncollinear spin DFT, (b) highly correlated materials (e.g., magnetite) using DFT+U, and (c) various spin states of ozone using coupled cluster expansions. The computed ASMs are in good agreement with available experimental results for a variety of periodic and nonperiodic materials. Examples considered include the antiferromagnetic metal organic framework Cu3(BTC)2, several ozone spin states, mono- and binuclear transition metal complexes, ferri- and ferro-magnetic solids (e.g., Fe3O4, Fe3Si), and simple molecular systems. We briefly discuss the theory of exchange-correlation functionals for studying noncollinear magnetism. A method for finding the ground state of systems with highly noncollinear magnetism is introduced. We use these methods to study the spin-orbit coupling potential energy surface of the single molecule magnet Fe4C40H52N4O12, which has highly noncollinear magnetism, and find that it contains unusual features that give a new interpretation to experimental data.
Computer Metaphors: Approaches to Computer Literacy for Educators.
ERIC Educational Resources Information Center
Peelle, Howard A.
Because metaphors offer ready perspectives for comprehending something new, this document examines various metaphors educators might use to help students develop computer literacy. Metaphors described are the computer as person (a complex system worthy of respect), tool (perhaps the most powerful and versatile known to humankind), brain (both…
NASA Technical Reports Server (NTRS)
Kory, Carol L.
1999-01-01
The phenomenal growth of commercial communications has created a great demand for traveling-wave tube (TWT) amplifiers. Although the helix slow-wave circuit remains the mainstay of the TWT industry because of its exceptionally wide bandwidth, until recently it has been impossible to accurately analyze a helical TWT using its exact dimensions because of the complexity of its geometrical structure. For the first time, an accurate three-dimensional helical model was developed that allows accurate prediction of TWT cold-test characteristics including operating frequency, interaction impedance, and attenuation. This computational model, which was developed at the NASA Lewis Research Center, allows TWT designers to obtain a more accurate value of interaction impedance than is possible using experimental methods. Obtaining helical slow-wave circuit interaction impedance is an important part of the design process for a TWT because it is related to the gain and efficiency of the tube. This impedance cannot be measured directly; thus, conventional methods involve perturbing a helical circuit with a cylindrical dielectric rod placed on the central axis of the circuit and obtaining the difference in resonant frequency between the perturbed and unperturbed circuits. A mathematical relationship has been derived between this frequency difference and the interaction impedance (ref. 1). However, because of the complex configuration of the helical circuit, deriving this relationship involves several approximations. In addition, this experimental procedure is time-consuming and expensive, but until recently it was widely accepted as the most accurate means of determining interaction impedance. The advent of an accurate three-dimensional helical circuit model (ref. 2) made it possible for Lewis researchers to fully investigate standard approximations made in deriving the relationship between measured perturbation data and interaction impedance. The most prominent approximations made
An accurate scheme to solve cluster dynamics equations using a Fokker-Planck approach
NASA Astrophysics Data System (ADS)
Jourdan, T.; Stoltz, G.; Legoll, F.; Monasse, L.
2016-10-01
We present a numerical method to accurately simulate particle size distributions within the formalism of rate equation cluster dynamics. This method is based on a discretization of the associated Fokker-Planck equation. We show that particular care has to be taken to discretize the advection part of the Fokker-Planck equation, in order to avoid distortions of the distribution due to numerical diffusion. For this purpose we use the Kurganov-Noelle-Petrova scheme coupled with the monotonicity-preserving reconstruction MP5, which leads to very accurate results. The interest of the method is highlighted in the case of loop coarsening in aluminum. We show that the choice of the models to describe the energetics of loops does not significantly change the normalized loop distribution, while the choice of the models for the absorption coefficients seems to have a significant impact on it.
An impedimetric approach for accurate particle sizing using a microfluidic Coulter counter
NASA Astrophysics Data System (ADS)
Jagtiani, Ashish V.; Carletta, Joan; Zhe, Jiang
2011-04-01
In this paper, we present the design, impedimetric characterization and testing of a microfabricated Coulter counter for particle size measurement that uses a pair of thin film coplanar Au/Ti electrodes. An electrical equivalent circuit model of the designed device is analyzed. Accurate measurement of particle size was achieved by operating the device at a frequency for which the overall impedance is dominated by the channel resistance. A combination of design features, including the use of a pair of sensing electrodes with a surface area of 100 µm by 435 µm, a spacing of 1785 µm between the two sensing electrodes and a 350 µm long microchannel, ensures that this resistance dominates over a range of relatively low frequencies. The device was characterized for NaCl electrolyte solutions with different ionic concentrations ranging from 10-5 to 0.1 M. Results proved that the resistive behavior of the sensor occurs over a range of relatively low frequencies for all tested concentrations. The Coulter counter was then used to detect 30 µm polystyrene particles at a selected excitation frequency. Testing results demonstrated that the device can accurately measure particle sizes with small error. The design can be extended to ac Coulter counters with sub-micron sensing channels. Analysis of three designs of ac Coulter counters including sub-micron sensing channels using the electrical equivalent circuit model predicts that they can be operated at even lower frequencies, to accurately size nanoscale particles.
Accurate Time-Dependent Traveling-Wave Tube Model Developed for Computational Bit-Error-Rate Testing
NASA Technical Reports Server (NTRS)
Kory, Carol L.
2001-01-01
The phenomenal growth of the satellite communications industry has created a large demand for traveling-wave tubes (TWT's) operating with unprecedented specifications requiring the design and production of many novel devices in record time. To achieve this, the TWT industry heavily relies on computational modeling. However, the TWT industry's computational modeling capabilities need to be improved because there are often discrepancies between measured TWT data and that predicted by conventional two-dimensional helical TWT interaction codes. This limits the analysis and design of novel devices or TWT's with parameters differing from what is conventionally manufactured. In addition, the inaccuracy of current computational tools limits achievable TWT performance because optimized designs require highly accurate models. To address these concerns, a fully three-dimensional, time-dependent, helical TWT interaction model was developed using the electromagnetic particle-in-cell code MAFIA (Solution of MAxwell's equations by the Finite-Integration-Algorithm). The model includes a short section of helical slow-wave circuit with excitation fed by radiofrequency input/output couplers, and an electron beam contained by periodic permanent magnet focusing. A cutaway view of several turns of the three-dimensional helical slow-wave circuit with input/output couplers is shown. This has been shown to be more accurate than conventionally used two-dimensional models. The growth of the communications industry has also imposed a demand for increased data rates for the transmission of large volumes of data. To achieve increased data rates, complex modulation and multiple access techniques are employed requiring minimum distortion of the signal as it is passed through the TWT. Thus, intersymbol interference (ISI) becomes a major consideration, as well as suspected causes such as reflections within the TWT. To experimentally investigate effects of the physical TWT on ISI would be
Gray, Alan; Harlen, Oliver G.; Harris, Sarah A.; Khalid, Syma; Leung, Yuk Ming; Lonsdale, Richard; Mulholland, Adrian J.; Pearson, Arwen R.; Read, Daniel J.; Richardson, Robin A.
2015-01-01
The current computational techniques available for biomolecular simulation are described, and the successes and limitations of each with reference to the experimental biophysical methods that they complement are presented. Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational.
Taverna, Ettore; Ufenast, Henri; Broffoni, Laura; Garavaglia, Guido
2013-01-01
The Latarjet procedure is a confirmed method for the treatment of shoulder instability in the presence of bone loss. It is a challenging procedure for which a key point is the correct placement of the coracoid graft onto the glenoid neck. We here present our technique for an athroscopically assisted Latarjet procedure with a new drill guide, permitting an accurate and reproducible positioning of the coracoid graft, with optimal compression of the graft onto the glenoid neck due to the perfect position of the screws: perpendicular to the graft and the glenoid neck and parallel between them. PMID:24167405
Taverna, Ettore; Ufenast, Henri; Broffoni, Laura; Garavaglia, Guido
2013-07-01
The Latarjet procedure is a confirmed method for the treatment of shoulder instability in the presence of bone loss. It is a challenging procedure for which a key point is the correct placement of the coracoid graft onto the glenoid neck. We here present our technique for an athroscopically assisted Latarjet procedure with a new drill guide, permitting an accurate and reproducible positioning of the coracoid graft, with optimal compression of the graft onto the glenoid neck due to the perfect position of the screws: perpendicular to the graft and the glenoid neck and parallel between them.
Accurate Vehicle Location System Using RFID, an Internet of Things Approach.
Prinsloo, Jaco; Malekian, Reza
2016-06-04
Modern infrastructure, such as dense urban areas and underground tunnels, can effectively block all GPS signals, which implies that effective position triangulation will not be achieved. The main problem that is addressed in this project is the design and implementation of an accurate vehicle location system using radio-frequency identification (RFID) technology in combination with GPS and the Global system for Mobile communication (GSM) technology, in order to provide a solution to the limitation discussed above. In essence, autonomous vehicle tracking will be facilitated with the use of RFID technology where GPS signals are non-existent. The design of the system and the results are reflected in this paper. An extensive literature study was done on the field known as the Internet of Things, as well as various topics that covered the integration of independent technology in order to address a specific challenge. The proposed system is then designed and implemented. An RFID transponder was successfully designed and a read range of approximately 31 cm was obtained in the low frequency communication range (125 kHz to 134 kHz). The proposed system was designed, implemented, and field tested and it was found that a vehicle could be accurately located and tracked. It is also found that the antenna size of both the RFID reader unit and RFID transponder plays a critical role in the maximum communication range that can be achieved.
Accurate Vehicle Location System Using RFID, an Internet of Things Approach.
Prinsloo, Jaco; Malekian, Reza
2016-01-01
Modern infrastructure, such as dense urban areas and underground tunnels, can effectively block all GPS signals, which implies that effective position triangulation will not be achieved. The main problem that is addressed in this project is the design and implementation of an accurate vehicle location system using radio-frequency identification (RFID) technology in combination with GPS and the Global system for Mobile communication (GSM) technology, in order to provide a solution to the limitation discussed above. In essence, autonomous vehicle tracking will be facilitated with the use of RFID technology where GPS signals are non-existent. The design of the system and the results are reflected in this paper. An extensive literature study was done on the field known as the Internet of Things, as well as various topics that covered the integration of independent technology in order to address a specific challenge. The proposed system is then designed and implemented. An RFID transponder was successfully designed and a read range of approximately 31 cm was obtained in the low frequency communication range (125 kHz to 134 kHz). The proposed system was designed, implemented, and field tested and it was found that a vehicle could be accurately located and tracked. It is also found that the antenna size of both the RFID reader unit and RFID transponder plays a critical role in the maximum communication range that can be achieved. PMID:27271638
Accurate Vehicle Location System Using RFID, an Internet of Things Approach
Prinsloo, Jaco; Malekian, Reza
2016-01-01
Modern infrastructure, such as dense urban areas and underground tunnels, can effectively block all GPS signals, which implies that effective position triangulation will not be achieved. The main problem that is addressed in this project is the design and implementation of an accurate vehicle location system using radio-frequency identification (RFID) technology in combination with GPS and the Global system for Mobile communication (GSM) technology, in order to provide a solution to the limitation discussed above. In essence, autonomous vehicle tracking will be facilitated with the use of RFID technology where GPS signals are non-existent. The design of the system and the results are reflected in this paper. An extensive literature study was done on the field known as the Internet of Things, as well as various topics that covered the integration of independent technology in order to address a specific challenge. The proposed system is then designed and implemented. An RFID transponder was successfully designed and a read range of approximately 31 cm was obtained in the low frequency communication range (125 kHz to 134 kHz). The proposed system was designed, implemented, and field tested and it was found that a vehicle could be accurately located and tracked. It is also found that the antenna size of both the RFID reader unit and RFID transponder plays a critical role in the maximum communication range that can be achieved. PMID:27271638
Measuring Attitudes toward Computers: Two Approaches
Kjerulff, K.H.; Counte, Michael A.
1984-01-01
The purpose of this paper is to present two questionnaires developed by the authors to measure attitudes toward computers. The first questionnaire is designed to measure attitudes toward computers in general. The second questionnaire is designed to assess attitudes toward a specific medical information system. Data concerning the reliability of these instruments is presented. Data concerning both the predictive and the concurrent validity of these measures are also presented. The results indicate that scores on both of the questionnaires assessed prior to computer implementation are reliable and valid predictors of post-implementation adaptation to the computer and perceptions of training. Scores on the questionnaires designed to assess specific attitudes, measured at three points in time, are also related to concurrent measures of job satisfaction and adaptation to the computer system.
Sansone, Giuseppe; Maschio, Lorenzo; Usvyat, Denis; Schütz, Martin; Karttunen, Antti
2016-01-01
The black phosphorus (black-P) crystal is formed of covalently bound layers of phosphorene stacked together by weak van der Waals interactions. An experimental measurement of the exfoliation energy of black-P is not available presently, making theoretical studies the most important source of information for the optimization of phosphorene production. Here, we provide an accurate estimate of the exfoliation energy of black-P on the basis of multilevel quantum chemical calculations, which include the periodic local Møller-Plesset perturbation theory of second order, augmented by higher-order corrections, which are evaluated with finite clusters mimicking the crystal. Very similar results are also obtained by density functional theory with the D3-version of Grimme's empirical dispersion correction. Our estimate of the exfoliation energy for black-P of -151 meV/atom is substantially larger than that of graphite, suggesting the need for different strategies to generate isolated layers for these two systems. PMID:26651397
Digital test signal generation: An accurate SNR calibration approach for the DSN
NASA Technical Reports Server (NTRS)
Gutierrez-Luaces, B. O.
1991-01-01
A new method of generating analog test signals with accurate signal to noise ratios (SNRs) is described. High accuracy will be obtained by simultaneous generation of digital noise and signal spectra at a given baseband or bandpass limited bandwidth. The digital synthesis will provide a test signal embedded in noise with the statistical properties of a stationary random process. Accuracy will only be dependent on test integration time with a limit imposed by the system quantization noise (expected to be 0.02 dB). Setability will be approximately 0.1 dB. The first digital SNR generator to provide baseband test signals is being built and will be available in early 1991.
Sansone, Giuseppe; Maschio, Lorenzo; Usvyat, Denis; Schütz, Martin; Karttunen, Antti
2016-01-01
The black phosphorus (black-P) crystal is formed of covalently bound layers of phosphorene stacked together by weak van der Waals interactions. An experimental measurement of the exfoliation energy of black-P is not available presently, making theoretical studies the most important source of information for the optimization of phosphorene production. Here, we provide an accurate estimate of the exfoliation energy of black-P on the basis of multilevel quantum chemical calculations, which include the periodic local Møller-Plesset perturbation theory of second order, augmented by higher-order corrections, which are evaluated with finite clusters mimicking the crystal. Very similar results are also obtained by density functional theory with the D3-version of Grimme's empirical dispersion correction. Our estimate of the exfoliation energy for black-P of -151 meV/atom is substantially larger than that of graphite, suggesting the need for different strategies to generate isolated layers for these two systems.
Hermosilla, Laura; Prampolini, Giacomo; Calle, Paloma; García de la Vega, José Manuel; Brancato, Giuseppe; Barone, Vincenzo
2015-01-01
A computational strategy that combines both time-dependent and time-independent approaches is exploited to accurately model molecular dynamics and solvent effects on the isotropic hyperfine coupling constants of the DMPO-H nitroxide. Our recent general force field for nitroxides derived from AMBER ff99SB is further extended to systems involving hydrogen atoms in β-positions with respect to NO. The resulting force-field has been employed in a series of classical molecular dynamics simulations, comparing the computed EPR parameters from selected molecular configurations to the corresponding experimental data in different solvents. The effect of vibrational averaging on the spectroscopic parameters is also taken into account, by second order vibrational perturbation theory involving semi-diagonal third energy derivatives together first and second property derivatives. PMID:26584116
Advances in Proteomics Data Analysis and Display Using an Accurate Mass and Time Tag Approach
Zimmer, Jennifer S.D.; Monroe, Matthew E.; Qian, Wei-Jun; Smith, Richard D.
2007-01-01
Proteomics has recently demonstrated utility in understanding cellular processes on the molecular level as a component of systems biology approaches and for identifying potential biomarkers of various disease states. The large amount of data generated by utilizing high efficiency (e.g., chromatographic) separations coupled to high mass accuracy mass spectrometry for high-throughput proteomics analyses presents challenges related to data processing, analysis, and display. This review focuses on recent advances in nanoLC-FTICR-MS-based proteomics approaches and the accompanying data processing tools that have been developed to display and interpret the large volumes of data being produced. PMID:16429408
Dynamical Approach Study of Spurious Numerics in Nonlinear Computations
NASA Technical Reports Server (NTRS)
Yee, H. C.; Mansour, Nagi (Technical Monitor)
2002-01-01
The last two decades have been an era when computation is ahead of analysis and when very large scale practical computations are increasingly used in poorly understood multiscale complex nonlinear physical problems and non-traditional fields. Ensuring a higher level of confidence in the predictability and reliability (PAR) of these numerical simulations could play a major role in furthering the design, understanding, affordability and safety of our next generation air and space transportation systems, and systems for planetary and atmospheric sciences, and in understanding the evolution and origin of life. The need to guarantee PAR becomes acute when computations offer the ONLY way of solving these types of data limited problems. Employing theory from nonlinear dynamical systems, some building blocks to ensure a higher level of confidence in PAR of numerical simulations have been revealed by the author and world expert collaborators in relevant fields. Five building blocks with supporting numerical examples were discussed. The next step is to utilize knowledge gained by including nonlinear dynamics, bifurcation and chaos theories as an integral part of the numerical process. The third step is to design integrated criteria for reliable and accurate algorithms that cater to the different multiscale nonlinear physics. This includes but is not limited to the construction of appropriate adaptive spatial and temporal discretizations that are suitable for the underlying governing equations. In addition, a multiresolution wavelets approach for adaptive numerical dissipation/filter controls for high speed turbulence, acoustics and combustion simulations will be sought. These steps are corner stones for guarding against spurious numerical solutions that are solutions of the discretized counterparts but are not solutions of the underlying governing equations.
An Accurate and Generic Testing Approach to Vehicle Stability Parameters Based on GPS and INS
Miao, Zhibin; Zhang, Hongtian; Zhang, Jinzhu
2015-01-01
With the development of the vehicle industry, controlling stability has become more and more important. Techniques of evaluating vehicle stability are in high demand. As a common method, usually GPS sensors and INS sensors are applied to measure vehicle stability parameters by fusing data from the two system sensors. Although prior model parameters should be recognized in a Kalman filter, it is usually used to fuse data from multi-sensors. In this paper, a robust, intelligent and precise method to the measurement of vehicle stability is proposed. First, a fuzzy interpolation method is proposed, along with a four-wheel vehicle dynamic model. Second, a two-stage Kalman filter, which fuses the data from GPS and INS, is established. Next, this approach is applied to a case study vehicle to measure yaw rate and sideslip angle. The results show the advantages of the approach. Finally, a simulation and real experiment is made to verify the advantages of this approach. The experimental results showed the merits of this method for measuring vehicle stability, and the approach can meet the design requirements of a vehicle stability controller. PMID:26690154
A Stationary Wavelet Entropy-Based Clustering Approach Accurately Predicts Gene Expression
Nguyen, Nha; Vo, An; Choi, Inchan
2015-01-01
Abstract Studying epigenetic landscapes is important to understand the condition for gene regulation. Clustering is a useful approach to study epigenetic landscapes by grouping genes based on their epigenetic conditions. However, classical clustering approaches that often use a representative value of the signals in a fixed-sized window do not fully use the information written in the epigenetic landscapes. Clustering approaches to maximize the information of the epigenetic signals are necessary for better understanding gene regulatory environments. For effective clustering of multidimensional epigenetic signals, we developed a method called Dewer, which uses the entropy of stationary wavelet of epigenetic signals inside enriched regions for gene clustering. Interestingly, the gene expression levels were highly correlated with the entropy levels of epigenetic signals. Dewer separates genes better than a window-based approach in the assessment using gene expression and achieved a correlation coefficient above 0.9 without using any training procedure. Our results show that the changes of the epigenetic signals are useful to study gene regulation. PMID:25383910
An efficient and accurate approach to MTE-MART for time-resolved tomographic PIV
NASA Astrophysics Data System (ADS)
Lynch, K. P.; Scarano, F.
2015-03-01
The motion-tracking-enhanced MART (MTE-MART; Novara et al. in Meas Sci Technol 21:035401, 2010) has demonstrated the potential to increase the accuracy of tomographic PIV by the combined use of a short sequence of non-simultaneous recordings. A clear bottleneck of the MTE-MART technique has been its computational cost. For large datasets comprising time-resolved sequences, MTE-MART becomes unaffordable and has been barely applied even for the analysis of densely seeded tomographic PIV datasets. A novel implementation is proposed for tomographic PIV image sequences, which strongly reduces the computational burden of MTE-MART, possibly below that of regular MART. The method is a sequential algorithm that produces a time-marching estimation of the object intensity field based on an enhanced guess, which is built upon the object reconstructed at the previous time instant. As the method becomes effective after a number of snapshots (typically 5-10), the sequential MTE-MART (SMTE) is most suited for time-resolved sequences. The computational cost reduction due to SMTE simply stems from the fewer MART iterations required for each time instant. Moreover, the method yields superior reconstruction quality and higher velocity field measurement precision when compared with both MART and MTE-MART. The working principle is assessed in terms of computational effort, reconstruction quality and velocity field accuracy with both synthetic time-resolved tomographic images of a turbulent boundary layer and two experimental databases documented in the literature. The first is the time-resolved data of flow past an airfoil trailing edge used in the study of Novara and Scarano (Exp Fluids 52:1027-1041, 2012); the second is a swirling jet in a water flow. In both cases, the effective elimination of ghost particles is demonstrated in number and intensity within a short temporal transient of 5-10 frames, depending on the seeding density. The increased value of the velocity space
NASA Astrophysics Data System (ADS)
Meng, Qingyong; Chen, Jun; Zhang, Dong H.
2016-04-01
To fast and accurately compute rate coefficients of the H/D + CH4 → H2/HD + CH3 reactions, we propose a segmented strategy for fitting suitable potential energy surface (PES), on which ring-polymer molecular dynamics (RPMD) simulations are performed. On the basis of recently developed permutation invariant polynomial neural-network approach [J. Li et al., J. Chem. Phys. 142, 204302 (2015)], PESs in local configuration spaces are constructed. In this strategy, global PES is divided into three parts, including asymptotic, intermediate, and interaction parts, along the reaction coordinate. Since less fitting parameters are involved in the local PESs, the computational efficiency for operating the PES routine is largely enhanced by a factor of ˜20, comparing with that for global PES. On interaction part, the RPMD computational time for the transmission coefficient can be further efficiently reduced by cutting off the redundant part of the child trajectories. For H + CH4, good agreements among the present RPMD rates and those from previous simulations as well as experimental results are found. For D + CH4, on the other hand, qualitative agreement between present RPMD and experimental results is predicted.
London, Nir; Ambroggio, Xavier
2014-02-01
Computational protein design efforts aim to create novel proteins and functions in an automated manner and, in the process, these efforts shed light on the factors shaping natural proteins. The focus of these efforts has progressed from the interior of proteins to their surface and the design of functions, such as binding or catalysis. Here we examine progress in the development of robust methods for the computational design of non-natural interactions between proteins and molecular targets such as other proteins or small molecules. This problem is referred to as the de novo computational design of interactions. Recent successful efforts in de novo enzyme design and the de novo design of protein-protein interactions open a path towards solving this problem. We examine the common themes in these efforts, and review recent studies aimed at understanding the nature of successes and failures in the de novo computational design of interactions. While several approaches culminated in success, the use of a well-defined structural model for a specific binding interaction in particular has emerged as a key strategy for a successful design, and is therefore reviewed with special consideration.
Baiardi, Alberto; Bloino, Julien; Barone, Vincenzo
2015-07-14
The interpretation and analysis of experimental resonance-Raman (RR) spectra can be significantly facilitated by vibronic computations based on reliable quantum-mechanical (QM) methods. With the aim of improving the description of large and flexible molecules, our recent time-dependent formulation to compute vibrationally resolved electronic spectra, based on Cartesian coordinates, has been extended to support internal coordinates. A set of nonredundant delocalized coordinates is automatically generated from the molecular connectivity thanks to a new general and robust procedure. In order to validate our implementation, a series of molecules has been used as test cases. Among them, rigid systems show that normal modes based on Cartesian and delocalized internal coordinates provide equivalent results, but the latter set is much more convenient and reliable for systems characterized by strong geometric deformations associated with the electronic transition. The so-called Z-matrix internal coordinates, which perform well for chain molecules, are also shown to be poorly suited in the presence of cycles or nonstandard structures.
An Approach to More Accurate Model Systems for Purple Acid Phosphatases (PAPs).
Bernhardt, Paul V; Bosch, Simone; Comba, Peter; Gahan, Lawrence R; Hanson, Graeme R; Mereacre, Valeriu; Noble, Christopher J; Powell, Annie K; Schenk, Gerhard; Wadepohl, Hubert
2015-08-01
The active site of mammalian purple acid phosphatases (PAPs) have a dinuclear iron site in two accessible oxidation states (Fe(III)2 and Fe(III)Fe(II)), and the heterovalent is the active form, involved in the regulation of phosphate and phosphorylated metabolite levels in a wide range of organisms. Therefore, two sites with different coordination geometries to stabilize the heterovalent active form and, in addition, with hydrogen bond donors to enable the fixation of the substrate and release of the product, are believed to be required for catalytically competent model systems. Two ligands and their dinuclear iron complexes have been studied in detail. The solid-state structures and properties, studied by X-ray crystallography, magnetism, and Mössbauer spectroscopy, and the solution structural and electronic properties, investigated by mass spectrometry, electronic, nuclear magnetic resonance (NMR), electron paramagnetic resonance (EPR), and Mössbauer spectroscopies and electrochemistry, are discussed in detail in order to understand the structures and relative stabilities in solution. In particular, with one of the ligands, a heterovalent Fe(III)Fe(II) species has been produced by chemical oxidation of the Fe(II)2 precursor. The phosphatase reactivities of the complexes, in particular, also of the heterovalent complex, are reported. These studies include pH-dependent as well as substrate concentration dependent studies, leading to pH profiles, catalytic efficiencies and turnover numbers, and indicate that the heterovalent diiron complex discussed here is an accurate PAP model system. PMID:26196255
Accurate Waveforms for Non-spinning Binary Black Holes using the Effective-one-body Approach
NASA Technical Reports Server (NTRS)
Buonanno, Alessandra; Pan, Yi; Baker, John G.; Centrella, Joan; Kelly, Bernard J.; McWilliams, Sean T.; vanMeter, James R.
2007-01-01
Using numerical relativity as guidance and the natural flexibility of the effective-one-body (EOB) model, we extend the latter so that it can successfully match the numerical relativity waveforms of non-spinning binary black holes during the last stages of inspiral, merger and ringdown. Here, by successfully, we mean with phase differences < or approx. 8% of a gravitational-wave cycle accumulated until the end of the ringdown phase. We obtain this result by simply adding a 4 post-Newtonian order correction in the EOB radial potential and determining the (constant) coefficient by imposing high-matching performances with numerical waveforms of mass ratios m1/m2 = 1,2/3,1/2 and = 1/4, m1 and m2 being the individual black-hole masses. The final black-hole mass and spin predicted by the numerical simulations are used to determine the ringdown frequency and decay time of three quasi-normal-mode damped sinusoids that are attached to the EOB inspiral-(plunge) waveform at the light-ring. The accurate EOB waveforms may be employed for coherent searches of gravitational waves emitted by non-spinning coalescing binary black holes with ground-based laser-interferometer detectors.
A Numerical Approach for Computing Standard Errors of Linear Equating.
ERIC Educational Resources Information Center
Zeng, Lingjia
1993-01-01
A numerical approach for computing standard errors (SEs) of a linear equating is described in which first partial derivatives of equating functions needed to compute SEs are derived numerically. Numerical and analytical approaches are compared using the Tucker equating method. SEs derived numerically are found indistinguishable from SEs derived…
Effective approach for accurately calculating individual energy of polar heterojunction interfaces
NASA Astrophysics Data System (ADS)
Akiyama, Toru; Nakane, Harunobu; Nakamura, Kohji; Ito, Tomonori
2016-09-01
We propose a direct approach for calculating individual energy of polar semiconductor interfaces using density functional theory calculations. This approach is applied to polar interfaces between group-III nitrides (AlN and GaN) and SiC and clarifies the interplay of chemical bonding and charge neutrality at the interface, which is crucial for the stability and polarity of group-III nitrides on SiC substrates. The ideal interface is stabilized among various atomic arrangements over the wide range of the chemical potential on Si-face SiC, whereas those with intermixing are favorable on C-face SiC. The stabilization of the ideal interfaces resulting in Ga-polar GaN and Al-polar AlN films on Si-face SiC is consistent with experiments, suggesting that our approach is versatile to evaluate various polar heterojunction interfaces as well as group-III nitrides on semiconductor substrates.
Computational dynamics for robotics systems using a non-strict computational approach
NASA Technical Reports Server (NTRS)
Orin, David E.; Wong, Ho-Cheung; Sadayappan, P.
1989-01-01
A Non-Strict computational approach for real-time robotics control computations is proposed. In contrast to the traditional approach to scheduling such computations, based strictly on task dependence relations, the proposed approach relaxes precedence constraints and scheduling is guided instead by the relative sensitivity of the outputs with respect to the various paths in the task graph. An example of the computation of the Inverse Dynamics of a simple inverted pendulum is used to demonstrate the reduction in effective computational latency through use of the Non-Strict approach. A speedup of 5 has been obtained when the processes of the task graph are scheduled to reduce the latency along the crucial path of the computation. While error is introduced by the relaxation of precedence constraints, the Non-Strict approach has a smaller error than the conventional Strict approach for a wide range of input conditions.
Computer-based Approaches to Patient Education
Lewis, Deborah
1999-01-01
All articles indexed in MEDLINE or CINAHL, related to the use of computer technology in patient education, and published in peer-reviewed journals between 1971 and 1998 were selected for review. Sixty-six articles, including 21 research-based reports, were identified. Forty-five percent of the studies were related to the management of chronic disease. Thirteen studies described an improvement in knowledge scores or clinical outcomes when computer-based patient education was compared with traditional instruction. Additional articles examined patients' computer experience, socioeconomic status, race, and gender and found no significant differences when compared with program outcomes. Sixteen of the 21 research-based studies had effect sizes greater than 0.5, indicating a significant change in the described outcome when the study subjects participated in computer-based patient education. The findings from this review support computer-based education as an effective strategy for transfer of knowledge and skill development for patients. The limited number of research studies (N = 21) points to the need for additional research. Recommendations for new studies include cost-benefit analysis and the impact of these new technologies on health outcomes over time. PMID:10428001
NASA Astrophysics Data System (ADS)
Stavrakoudis, Dimitris; Gitas, Ioannis; Karydas, Christos; Kolokoussis, Polychronis; Karathanassi, Vassilia
2015-10-01
This paper proposes an efficient methodology for combining multiple remotely sensed imagery, in order to increase the classification accuracy in complex forest species mapping tasks. The proposed scheme follows a decision fusion approach, whereby each image is first classified separately by means of a pixel-wise Fuzzy-Output Support Vector Machine (FO-SVM) classifier. Subsequently, the multiple results are fused according to the so-called multiple spectral- spatial classifier using the minimum spanning forest (MSSC-MSF) approach, which constitutes an effective post-regularization procedure for enhancing the result of a single pixel-based classification. For this purpose, the original MSSC-MSF has been extended in order to handle multiple classifications. In particular, the fuzzy outputs of the pixel-based classifiers are stacked and used to grow the MSF, whereas the markers are also determined considering both classifications. The proposed methodology has been tested on a challenging forest species mapping task in northern Greece, considering a multispectral (GeoEye) and a hyper-spectral (CASI) image. The pixel-wise classifications resulted in overall accuracies (OA) of 68.71% for the GeoEye and 77.95% for the CASI images, respectively. Both of them are characterized by high levels of speckle noise. Applying the proposed multi-source MSSC-MSF fusion, the OA climbs to 90.86%, which is attributed both to the ability of MSSC-MSF to tackle the salt-and-pepper effect, as well as the fact that the fusion approach exploits the relative advantages of both information sources.
Human brain mapping: Experimental and computational approaches
Wood, C.C.; George, J.S.; Schmidt, D.M.; Aine, C.J.; Sanders, J.; Belliveau, J.
1998-11-01
This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). This program developed project combined Los Alamos' and collaborators' strengths in noninvasive brain imaging and high performance computing to develop potential contributions to the multi-agency Human Brain Project led by the National Institute of Mental Health. The experimental component of the project emphasized the optimization of spatial and temporal resolution of functional brain imaging by combining: (a) structural MRI measurements of brain anatomy; (b) functional MRI measurements of blood flow and oxygenation; and (c) MEG measurements of time-resolved neuronal population currents. The computational component of the project emphasized development of a high-resolution 3-D volumetric model of the brain based on anatomical MRI, in which structural and functional information from multiple imaging modalities can be integrated into a single computational framework for modeling, visualization, and database representation.
A Proposed Frequency Synthesis Approach to Accurately Measure the Angular Position of a Spacecraft
NASA Technical Reports Server (NTRS)
Bagri, D. S.
2005-01-01
This article describes an approach for measuring the angular position of a spacecraft with reference to a nearby calibration source (quasar) with an accuracy of a few tenths of a nanoradian using a very long baseline interferometer of two antennas that measures the interferometer phase with a modest accuracy. It employs (1) radio frequency phase to determine the spacecraft position with high precision and (2) multiple delay measurements using either frequency tones or telemetry signals at different frequency spacings to resolve ambiguity of the location of the fringe (cycle) containing the direction of the spacecraft.
Efficient and accurate approach to modeling the microstructure and defect properties of LaCoO3
NASA Astrophysics Data System (ADS)
Buckeridge, J.; Taylor, F. H.; Catlow, C. R. A.
2016-04-01
Complex perovskite oxides are promising materials for cathode layers in solid oxide fuel cells. Such materials have intricate electronic, magnetic, and crystalline structures that prove challenging to model accurately. We analyze a wide range of standard density functional theory approaches to modeling a highly promising system, the perovskite LaCoO3, focusing on optimizing the Hubbard U parameter to treat the self-interaction of the B-site cation's d states, in order to determine the most appropriate method to study defect formation and the effect of spin on local structure. By calculating structural and electronic properties for different magnetic states we determine that U =4 eV for Co in LaCoO3 agrees best with available experiments. We demonstrate that the generalized gradient approximation (PBEsol +U ) is most appropriate for studying structure versus spin state, while the local density approximation (LDA +U ) is most appropriate for determining accurate energetics for defect properties.
NASA Astrophysics Data System (ADS)
Ford, Logan; Bajpayee, Abhishek; Techet, Alexandra
2015-11-01
3D particle image velocimetry (PIV) is becoming a popular technique to study biological flows. PIV images that contain fish or other animals around which flow is being studied, need to be appropriately masked in order to remove the animal body from the 3D reconstructed volumes prior to calculating particle displacement vectors. Presented here is a machine learning and synthetic aperture (SA) refocusing based approach for more accurate masking of fish from reconstructed intensity fields for 3D PIV purposes. Using prior knowledge about the 3D shape and appearance of the fish along with SA refocused images at arbitrarily oriented focal planes, the location and orientation of a fish in a reconstructed volume can be accurately determined. Once the location and orientation of a fish in a volume is determined, it can be masked out.
Computed tomography in trauma: An atlas approach
Toombs, B.D.; Sandler, C.
1986-01-01
This book discussed computed tomography in trauma. The text is organized according to mechanism of injury and site of injury. In addition to CT, some correlation with other imaging modalities is included. Blunt trauma, penetrating trauma, complications and sequelae of trauma, and use of other modalities are covered.
An Approach to Developing Computer Catalogs
ERIC Educational Resources Information Center
MacDonald, Robin W.; Elrod, J. McRee
1973-01-01
A method of developing computer catalogs is proposed which does not require unit card conversion but rather the accumulation of data from operating programs. It is proposed that the bibliographic and finding functions of the catalog be separated, with the latter being the first automated. (8 references) (Author)
Jaki, Thomas; Allacher, Peter; Horling, Frank
2016-09-01
Detecting and characterizing of anti-drug antibodies (ADA) against a protein therapeutic are crucially important to monitor the unwanted immune response. Usually a multi-tiered approach that initially rapidly screens for positive samples that are subsequently confirmed in a separate assay is employed for testing of patient samples for ADA activity. In this manuscript we evaluate the ability of different methods used to classify subject with screening and competition based confirmatory assays. We find that for the overall performance of the multi-stage process the method used for confirmation is most important where a t-test is best when differences are moderate to large. Moreover we find that, when differences between positive and negative samples are not sufficiently large, using a competition based confirmation step does yield poor classification of positive samples. PMID:27262992
NASA Astrophysics Data System (ADS)
Xu, Li; Weng, Peifen
2014-02-01
An improved fifth-order weighted essentially non-oscillatory (WENO-Z) scheme combined with the moving overset grid technique has been developed to compute unsteady compressible viscous flows on the helicopter rotor in forward flight. In order to enforce periodic rotation and pitching of the rotor and relative motion between rotor blades, the moving overset grid technique is extended, where a special judgement standard is presented near the odd surface of the blade grid during search donor cells by using the Inverse Map method. The WENO-Z scheme is adopted for reconstructing left and right state values with the Roe Riemann solver updating the inviscid fluxes and compared with the monotone upwind scheme for scalar conservation laws (MUSCL) and the classical WENO scheme. Since the WENO schemes require a six point stencil to build the fifth-order flux, the method of three layers of fringes for hole boundaries and artificial external boundaries is proposed to carry out flow information exchange between chimera grids. The time advance on the unsteady solution is performed by the full implicit dual time stepping method with Newton type LU-SGS subiteration, where the solutions of pseudo steady computation are as the initial fields of the unsteady flow computation. Numerical results on non-variable pitch rotor and periodic variable pitch rotor in forward flight reveal that the approach can effectively capture vortex wake with low dissipation and reach periodic solutions very soon.
PSI: A Comprehensive and Integrative Approach for Accurate Plant Subcellular Localization Prediction
Chen, Ming
2013-01-01
Predicting the subcellular localization of proteins conquers the major drawbacks of high-throughput localization experiments that are costly and time-consuming. However, current subcellular localization predictors are limited in scope and accuracy. In particular, most predictors perform well on certain locations or with certain data sets while poorly on others. Here, we present PSI, a novel high accuracy web server for plant subcellular localization prediction. PSI derives the wisdom of multiple specialized predictors via a joint-approach of group decision making strategy and machine learning methods to give an integrated best result. The overall accuracy obtained (up to 93.4%) was higher than best individual (CELLO) by ∼10.7%. The precision of each predicable subcellular location (more than 80%) far exceeds that of the individual predictors. It can also deal with multi-localization proteins. PSI is expected to be a powerful tool in protein location engineering as well as in plant sciences, while the strategy employed could be applied to other integrative problems. A user-friendly web server, PSI, has been developed for free access at http://bis.zju.edu.cn/psi/. PMID:24194827
Robust and Accurate Modeling Approaches for Migraine Per-Patient Prediction from Ambulatory Data
Pagán, Josué; Irene De Orbe, M.; Gago, Ana; Sobrado, Mónica; Risco-Martín, José L.; Vivancos Mora, J.; Moya, José M.; Ayala, José L.
2015-01-01
Migraine is one of the most wide-spread neurological disorders, and its medical treatment represents a high percentage of the costs of health systems. In some patients, characteristic symptoms that precede the headache appear. However, they are nonspecific, and their prediction horizon is unknown and pretty variable; hence, these symptoms are almost useless for prediction, and they are not useful to advance the intake of drugs to be effective and neutralize the pain. To solve this problem, this paper sets up a realistic monitoring scenario where hemodynamic variables from real patients are monitored in ambulatory conditions with a wireless body sensor network (WBSN). The acquired data are used to evaluate the predictive capabilities and robustness against noise and failures in sensors of several modeling approaches. The obtained results encourage the development of per-patient models based on state-space models (N4SID) that are capable of providing average forecast windows of 47 min and a low rate of false positives. PMID:26134103
NASA Astrophysics Data System (ADS)
Balabin, Roman M.; Lomakina, Ekaterina I.
2009-08-01
Artificial neural network (ANN) approach has been applied to estimate the density functional theory (DFT) energy with large basis set using lower-level energy values and molecular descriptors. A total of 208 different molecules were used for the ANN training, cross validation, and testing by applying BLYP, B3LYP, and BMK density functionals. Hartree-Fock results were reported for comparison. Furthermore, constitutional molecular descriptor (CD) and quantum-chemical molecular descriptor (QD) were used for building the calibration model. The neural network structure optimization, leading to four to five hidden neurons, was also carried out. The usage of several low-level energy values was found to greatly reduce the prediction error. An expected error, mean absolute deviation, for ANN approximation to DFT energies was 0.6±0.2 kcal mol-1. In addition, the comparison of the different density functionals with the basis sets and the comparison of multiple linear regression results were also provided. The CDs were found to overcome limitation of the QD. Furthermore, the effective ANN model for DFT/6-311G(3df,3pd) and DFT/6-311G(2df,2pd) energy estimation was developed, and the benchmark results were provided.
Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Egidi, Franco; Puzzarini, Cristina
2015-01-01
The CCSD(T) model coupled with extrapolation to the complete basis-set limit and additive approaches represents the “golden standard” for the structural and spectroscopic characterization of building blocks of biomolecules and nanosystems. However, when open-shell systems are considered, additional problems related to both specific computational difficulties and the need of obtaining spin-dependent properties appear. In this contribution, we present a comprehensive study of the molecular structure and spectroscopic (IR, Raman, EPR) properties of the phenyl radical with the aim of validating an accurate computational protocol able to deal with conjugated open-shell species. We succeeded in obtaining reliable and accurate results, thus confirming and, partly, extending the available experimental data. The main issue to be pointed out is the need of going beyond the CCSD(T) level by including a full treatment of triple excitations in order to fulfil the accuracy requirements. On the other hand, the reliability of density functional theory in properly treating open-shell systems has been further confirmed. PMID:23802956
Multicomputer approach to non-numeric computation
Baru, C.K.
1985-01-01
The architecture of a dynamically partitionable multicomputer system with switchable main memory modules (SM3) for non-numeric computations is studied. The architecture supports efficient execution of parallel algorithms for database processing by (i) allowing the sharing of switchable main memory modules between computers, (ii) supporting network partitioning, and (iii) employing global control lines to efficiently support interprocessor communication. The data transfer time is reduced to memory switching time by allowing some main memory modules to be switched between processors. Network partitioning gives a common bus network system to the capability of an MIMD machine while performing global operations. The global control lines establish a quick and efficient hig-level protocol in the system. The network is supervised by a control computer which oversees network partitioning and other functions. A simulation study of some commonly used database operations, using discrete-event simulation techniques, was carried out, and results of the study are presented. Certain aspects of the system architecture were modified on the basis of simulation results. The general-purpose nature of the SM3 system allows the implementation of a variety of parallel algorithms for database processing.
NASA Astrophysics Data System (ADS)
Zhang, Bin; Liang, Chunlei
2015-08-01
This paper presents a simple, efficient, and high-order accurate sliding-mesh interface approach to the spectral difference (SD) method. We demonstrate the approach by solving the two-dimensional compressible Navier-Stokes equations on quadrilateral grids. This approach is an extension of the straight mortar method originally designed for stationary domains [7,8]. Our sliding method creates curved dynamic mortars on sliding-mesh interfaces to couple rotating and stationary domains. On the nonconforming sliding-mesh interfaces, the related variables are first projected from cell faces to mortars to compute common fluxes, and then the common fluxes are projected back from the mortars to the cell faces to ensure conservation. To verify the spatial order of accuracy of the sliding-mesh spectral difference (SSD) method, both inviscid and viscous flow cases are tested. It is shown that the SSD method preserves the high-order accuracy of the SD method. Meanwhile, the SSD method is found to be very efficient in terms of computational cost. This novel sliding-mesh interface method is very suitable for parallel processing with domain decomposition. It can be applied to a wide range of problems, such as the hydrodynamics of marine propellers, the aerodynamics of rotorcraft, wind turbines, and oscillating wing power generators, etc.
A Social Construction Approach to Computer Science Education
ERIC Educational Resources Information Center
Machanick, Philip
2007-01-01
Computer science education research has mostly focused on cognitive approaches to learning. Cognitive approaches to understanding learning do not account for all the phenomena observed in teaching and learning. A number of apparently successful educational approaches, such as peer assessment, apprentice-based learning and action learning, have…
Fu, Jian; Tan, Renbo; Chen, Liyuan
2014-01-01
X-ray differential phase-contrast computed tomography (DPC-CT) is a powerful physical and biochemical analysis tool. In practical applications, there are often challenges for DPC-CT due to insufficient data caused by few-view, bad or missing detector channels, or limited scanning angular range. They occur quite frequently because of experimental constraints from imaging hardware, scanning geometry, and the exposure dose delivered to living specimens. In this work, we analyze the influence of incomplete data on DPC-CT image reconstruction. Then, a reconstruction method is developed and investigated for incomplete data DPC-CT. It is based on an algebraic iteration reconstruction technique, which minimizes the image total variation and permits accurate tomographic imaging with less data. This work comprises a numerical study of the method and its experimental verification using a dataset measured at the W2 beamline of the storage ring DORIS III equipped with a Talbot-Lau interferometer. The numerical and experimental results demonstrate that the presented method can handle incomplete data. It will be of interest for a wide range of DPC-CT applications in medicine, biology, and nondestructive testing.
Kong, Hao; Ma, Zhuoran; Wang, Song; Gong, Xiaoyun; Zhang, Sichun; Zhang, Xinrong
2014-08-01
With the inspiration of an ancient Chinese poison test approach, we report a rapid hydrogen sulfide detection strategy in specific areas of live cells using silver needles with good spatial resolution of 2 × 2 μm(2). Besides the accurate-localization ability, this reflection-based strategy also has attractive merits of convenience and robust response when free pretreatment and short detection time are concerned. The success of endogenous H2S level evaluation in cellular cytoplasm and nuclear of human A549 cells promises the application potential of our strategy in scientific research and medical diagnosis.
NASA Technical Reports Server (NTRS)
Lindner, Bernhard Lee; Ackerman, Thomas P.; Pollack, James B.
1990-01-01
CO2 comprises 95 pct. of the composition of the Martian atmosphere. However, the Martian atmosphere also has a high aerosol content. Dust particles vary from less than 0.2 to greater than 3.0. CO2 is an active absorber and emitter in near IR and IR wavelengths; the near IR absorption bands of CO2 provide significant heating of the atmosphere, and the 15 micron band provides rapid cooling. Including both CO2 and aerosol radiative transfer simultaneously in a model is difficult. Aerosol radiative transfer requires a multiple scattering code, while CO2 radiative transfer must deal with complex wavelength structure. As an alternative to the pure atmosphere treatment in most models which causes inaccuracies, a treatment was developed called the exponential sum or k distribution approximation. The chief advantage of the exponential sum approach is that the integration over k space of f(k) can be computed more quickly than the integration of k sub upsilon over frequency. The exponential sum approach is superior to the photon path distribution and emissivity techniques for dusty conditions. This study was the first application of the exponential sum approach to Martian conditions.
Information theoretic approaches to multidimensional neural computations
NASA Astrophysics Data System (ADS)
Fitzgerald, Jeffrey D.
Many systems in nature process information by transforming inputs from their environments into observable output states. These systems are often difficult to study because they are performing computations on multidimensional inputs with many degrees of freedom using highly nonlinear functions. The work presented in this dissertation deals with some of the issues involved with characterizing real-world input/output systems and understanding the properties of idealized systems using information theoretic methods. Using the principle of maximum entropy, a family of models are created that are consistent with certain measurable correlations from an input/output dataset but are maximally unbiased in all other respects, thereby eliminating all unjustified assumptions about the computation. In certain cases, including spiking neurons, we show that these models also minimize the mutual information. This property gives one the advantage of being able to identify the relevant input/output statistics by calculating their information content. We argue that these maximum entropy models provide a much needed quantitative framework for characterizing and understanding sensory processing neurons that are selective for multiple stimulus features. To demonstrate their usefulness, these ideas are applied to neural recordings from macaque retina and thalamus. These neurons, which primarily respond to two stimulus features, are shown to be well described using only first and second order statistics, indicating that their firing rates encode information about stimulus correlations. In addition to modeling multi-feature computations in the relevant feature space, we also show that maximum entropy models are capable of discovering the relevant feature space themselves. This technique overcomes the disadvantages of two commonly used dimensionality reduction methods and is explored using several simulated neurons, as well as retinal and thalamic recordings. Finally, we ask how neurons in a
Functional quantum computing: An optical approach
NASA Astrophysics Data System (ADS)
Rambo, Timothy M.; Altepeter, Joseph B.; Kumar, Prem; D'Ariano, G. Mauro
2016-05-01
Recent theoretical investigations treat quantum computations as functions, quantum processes which operate on other quantum processes, rather than circuits. Much attention has been given to the N -switch function which takes N black-box quantum operators as input, coherently permutes their ordering, and applies the result to a target quantum state. This is something which cannot be equivalently done using a quantum circuit. Here, we propose an all-optical system design which implements coherent operator permutation for an arbitrary number of input operators.
A Computational Approach to Competitive Range Expansions
NASA Astrophysics Data System (ADS)
Weber, Markus F.; Poxleitner, Gabriele; Hebisch, Elke; Frey, Erwin; Opitz, Madeleine
2014-03-01
Bacterial communities represent complex and dynamic ecological systems. Environmental conditions and microbial interactions determine whether a bacterial strain survives an expansion to new territory. In our work, we studied competitive range expansions in a model system of three Escherichia coli strains. In this system, a colicin producing strain competed with a colicin resistant, and with a colicin sensitive strain for new territory. Genetic engineering allowed us to tune the strains' growth rates and to study their expansion in distinct ecological scenarios (with either cyclic or hierarchical dominance). The control over growth rates also enabled us to construct and to validate a predictive computational model of the bacterial dynamics. The model rested on an agent-based, coarse-grained description of the expansion process and we conducted independent experiments on the growth of single-strain colonies for its parametrization. Furthermore, the model considered the long-range nature of the toxin interaction between strains. The integration of experimental analysis with computational modeling made it possible to quantify how the level of biodiversity depends on the interplay between bacterial growth rates, the initial composition of the inoculum, and the toxin range.
Computational approaches to homogeneous gold catalysis.
Faza, Olalla Nieto; López, Carlos Silva
2015-01-01
Homogenous gold catalysis has been exploding for the last decade at an outstanding pace. The best described reactivity of Au(I) and Au(III) species is based on gold's properties as a soft Lewis acid, but new reactivity patterns have recently emerged which further expand the range of transformations achievable using gold catalysis, with examples of dual gold activation, hydrogenation reactions, or Au(I)/Au(III) catalytic cycles.In this scenario, to develop fully all these new possibilities, the use of computational tools to understand at an atomistic level of detail the complete role of gold as a catalyst is unavoidable. In this work we aim to provide a comprehensive review of the available benchmark works on methodological options to study homogenous gold catalysis in the hope that this effort can help guide the choice of method in future mechanistic studies involving gold complexes. This is relevant because a representative number of current mechanistic studies still use methods which have been reported as inappropriate and dangerously inaccurate for this chemistry.Together with this, we describe a number of recent mechanistic studies where computational chemistry has provided relevant insights into non-conventional reaction paths, unexpected selectivities or novel reactivity, which illustrate the complexity behind gold-mediated organic chemistry.
Niklasson, Markus; Ahlner, Alexandra; Andresen, Cecilia; Marsh, Joseph A; Lundström, Patrik
2015-01-01
The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available.
Niklasson, Markus; Ahlner, Alexandra; Andresen, Cecilia; Marsh, Joseph A.; Lundström, Patrik
2015-01-01
The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available. PMID:25569628
Niklasson, Markus; Ahlner, Alexandra; Andresen, Cecilia; Marsh, Joseph A; Lundström, Patrik
2015-01-01
The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available. PMID:25569628
Novel Computational Approaches to Drug Discovery
NASA Astrophysics Data System (ADS)
Skolnick, Jeffrey; Brylinski, Michal
2010-01-01
New approaches to protein functional inference based on protein structure and evolution are described. First, FINDSITE, a threading based approach to protein function prediction, is summarized. Then, the results of large scale benchmarking of ligand binding site prediction, ligand screening, including applications to HIV protease, and GO molecular functional inference are presented. A key advantage of FINDSITE is its ability to use low resolution, predicted structures as well as high resolution experimental structures. Then, an extension of FINDSITE to ligand screening in GPCRs using predicted GPCR structures, FINDSITE/QDOCKX, is presented. This is a particularly difficult case as there are few experimentally solved GPCR structures. Thus, we first train on a subset of known binding ligands for a set of GPCRs; this is then followed by benchmarking against a large ligand library. For the virtual ligand screening of a number of Dopamine receptors, encouraging results are seen, with significant enrichment in identified ligands over those found in the training set. Thus, FINDSITE and its extensions represent a powerful approach to the successful prediction of a variety of molecular functions.
Computational approaches to natural product discovery.
Medema, Marnix H; Fischbach, Michael A
2015-09-01
Starting with the earliest Streptomyces genome sequences, the promise of natural product genome mining has been captivating: genomics and bioinformatics would transform compound discovery from an ad hoc pursuit to a high-throughput endeavor. Until recently, however, genome mining has advanced natural product discovery only modestly. Here, we argue that the development of algorithms to mine the continuously increasing amounts of (meta)genomic data will enable the promise of genome mining to be realized. We review computational strategies that have been developed to identify biosynthetic gene clusters in genome sequences and predict the chemical structures of their products. We then discuss networking strategies that can systematize large volumes of genetic and chemical data and connect genomic information to metabolomic and phenotypic data. Finally, we provide a vision of what natural product discovery might look like in the future, specifically considering longstanding questions in microbial ecology regarding the roles of metabolites in interspecies interactions.
Metabolomics and diabetes: analytical and computational approaches.
Sas, Kelli M; Karnovsky, Alla; Michailidis, George; Pennathur, Subramaniam
2015-03-01
Diabetes is characterized by altered metabolism of key molecules and regulatory pathways. The phenotypic expression of diabetes and associated complications encompasses complex interactions between genetic, environmental, and tissue-specific factors that require an integrated understanding of perturbations in the network of genes, proteins, and metabolites. Metabolomics attempts to systematically identify and quantitate small molecule metabolites from biological systems. The recent rapid development of a variety of analytical platforms based on mass spectrometry and nuclear magnetic resonance have enabled identification of complex metabolic phenotypes. Continued development of bioinformatics and analytical strategies has facilitated the discovery of causal links in understanding the pathophysiology of diabetes and its complications. Here, we summarize the metabolomics workflow, including analytical, statistical, and computational tools, highlight recent applications of metabolomics in diabetes research, and discuss the challenges in the field. PMID:25713200
Computational approaches to natural product discovery
Medema, Marnix H.; Fischbach, Michael A.
2016-01-01
From the earliest Streptomyces genome sequences, the promise of natural product genome mining has been captivating: genomics and bioinformatics would transform compound discovery from an ad hoc pursuit to a high-throughput endeavor. Until recently, however, genome mining has advanced natural product discovery only modestly. Here, we argue that the development of algorithms to mine the continuously increasing amounts of (meta)genomic data will enable the promise of genome mining to be realized. We review computational strategies that have been developed to identify biosynthetic gene clusters in genome sequences and predict the chemical structures of their products. We then discuss networking strategies that can systematize large volumes of genetic and chemical data, and connect genomic information to metabolomic and phenotypic data. Finally, we provide a vision of what natural product discovery might look like in the future, specifically considering long-standing questions in microbial ecology regarding the roles of metabolites in interspecies interactions. PMID:26284671
Metabolomics and Diabetes: Analytical and Computational Approaches
Sas, Kelli M.; Karnovsky, Alla; Michailidis, George
2015-01-01
Diabetes is characterized by altered metabolism of key molecules and regulatory pathways. The phenotypic expression of diabetes and associated complications encompasses complex interactions between genetic, environmental, and tissue-specific factors that require an integrated understanding of perturbations in the network of genes, proteins, and metabolites. Metabolomics attempts to systematically identify and quantitate small molecule metabolites from biological systems. The recent rapid development of a variety of analytical platforms based on mass spectrometry and nuclear magnetic resonance have enabled identification of complex metabolic phenotypes. Continued development of bioinformatics and analytical strategies has facilitated the discovery of causal links in understanding the pathophysiology of diabetes and its complications. Here, we summarize the metabolomics workflow, including analytical, statistical, and computational tools, highlight recent applications of metabolomics in diabetes research, and discuss the challenges in the field. PMID:25713200
Computational Approaches for Understanding Energy Metabolism
Shestov, Alexander A; Barker, Brandon; Gu, Zhenglong; Locasale, Jason W
2013-01-01
There has been a surge of interest in understanding the regulation of metabolic networks involved in disease in recent years. Quantitative models are increasingly being used to i nterrogate the metabolic pathways that are contained within this complex disease biology. At the core of this effort is the mathematical modeling of central carbon metabolism involving glycolysis and the citric acid cycle (referred to as energy metabolism). Here we discuss several approaches used to quantitatively model metabolic pathways relating to energy metabolism and discuss their formalisms, successes, and limitations. PMID:23897661
Alecu, I M; Truhlar, Donald G
2011-12-29
Multistructural canonical variational-transition-state theory with multidimensional tunneling (MS-CVT/MT) is employed to calculate thermal rate constants for the abstraction of hydrogen atoms from both positions of methanol by the hydroperoxyl and methyl radicals over the temperature range 100-3000 K. The M08-HX hybrid meta-generalized gradient approximation density functional and M08-HX with specific reaction parameters, both with the maug-cc-pVTZ basis set, were validated in part 1 of this study (Alecu, I. M.; Truhlar, D. G. J. Phys. Chem. A2011, 115, 2811) against highly accurate CCSDT(2)(Q)/CBS calculations for the energetics of these reactions, and they are used here to compute the properties of all stationary points and the energies, gradients, and Hessians of nonstationary points along each considered reaction path. The internal rotations in some of the transition states are found to be highly anharmonic and strongly coupled to each other, and they generate multiple structures (conformations) whose contributions are included in the partition function. It is shown that the previous estimates for these rate constants used to build kinetic models for the combustion of methanol, some of which were based on transition state theory calculations with one-dimensional tunneling corrections and harmonic-oscillator approximations or separable one-dimensional hindered rotor treatments of torsions, are appreciably different than the ones presently calculated using MS-CVT/MT. The rate constants obtained from the best MS-CVT/MT calculations carried out in this study, in which the important effects of corner cutting due to small and large reaction path curvature are captured via a microcanonical optimized multidimensional tunneling (μOMT) treatment, are recommended for future refinement of the kinetic model for methanol combustion. PMID:22059377
Mueller, Thomas L; Christen, David; Sandercott, Steve; Boyd, Steven K; van Rietbergen, Bert; Eckstein, Felix; Lochmüller, Eva-Maria; Müller, Ralph; van Lenthe, G Harry
2011-06-01
High-resolution peripheral quantitative computed tomography (HR-pQCT) is clinically available today and provides a non-invasive measure of 3D bone geometry and micro-architecture with unprecedented detail. In combination with microarchitectural finite element (μFE) models it can be used to determine bone strength using a strain-based failure criterion. Yet, images from only a relatively small part of the radius are acquired and it is not known whether the region recommended for clinical measurements does predict forearm fracture load best. Furthermore, it is questionable whether the currently used failure criterion is optimal because of improvements in image resolution, changes in the clinically measured volume of interest, and because the failure criterion depends on the amount of bone present. Hence, we hypothesized that bone strength estimates would improve by measuring a region closer to the subchondral plate, and by defining a failure criterion that would be independent of the measured volume of interest. To answer our hypotheses, 20% of the distal forearm length from 100 cadaveric but intact human forearms was measured using HR-pQCT. μFE bone strength was analyzed for different subvolumes, as well as for the entire 20% of the distal radius length. Specifically, failure criteria were developed that provided accurate estimates of bone strength as assessed experimentally. It was shown that distal volumes were better in predicting bone strength than more proximal ones. Clinically speaking, this would argue to move the volume of interest for the HR-pQCT measurements even more distally than currently recommended by the manufacturer. Furthermore, new parameter settings using the strain-based failure criterion are presented providing better accuracy for bone strength estimates.
A Social Constructivist Approach to Computer-Mediated Instruction.
ERIC Educational Resources Information Center
Pear, Joseph J.; Crone-Todd, Darlene E.
2002-01-01
Describes a computer-mediated teaching system called computer-aided personalized system of instruction (CAPSI) that incorporates a social constructivist approach, maintaining that learning occurs primarily through a socially interactive process. Discusses use of CAPSI in an undergraduate course at the University of Manitoba that showed students…
Hyperdimensional Computing Approach to Word Sense Disambiguation
Berster, Bjoern-Toby; Goodwin, J Caleb; Cohen, Trevor
2012-01-01
Coping with the ambiguous meanings of words has long been a hurdle for information retrieval and natural language processing systems. This paper presents a new word sense disambiguation approach using high-dimensional binary vectors, which encode meanings of words based on the different contexts in which they occur. In our approach, a randomly constructed vector is assigned to each ambiguous term, and another to each sense of this term. In the context of a sense-annotated training set, a reversible vector transformation is used to combine these vectors, such that both the term and the sense assigned to a context in which the term occurs are encoded into vectors representing the surrounding terms in this context. When a new context is encountered, the information required to disambiguate this term is extracted from the trained semantic vectors for the terms in this context by reversing the vector transformation to recover the correct sense of the term. On repeated experiments using ten-fold cross-validation and a standard test set, we obtained results comparable to the best obtained in previous studies. These results demonstrate the potential of our methodology, and suggest directions for future research. PMID:23304389
Multivariate analysis: A statistical approach for computations
NASA Astrophysics Data System (ADS)
Michu, Sachin; Kaushik, Vandana
2014-10-01
Multivariate analysis is a type of multivariate statistical approach commonly used in, automotive diagnosis, education evaluating clusters in finance etc and more recently in the health-related professions. The objective of the paper is to provide a detailed exploratory discussion about factor analysis (FA) in image retrieval method and correlation analysis (CA) of network traffic. Image retrieval methods aim to retrieve relevant images from a collected database, based on their content. The problem is made more difficult due to the high dimension of the variable space in which the images are represented. Multivariate correlation analysis proposes an anomaly detection and analysis method based on the correlation coefficient matrix. Anomaly behaviors in the network include the various attacks on the network like DDOs attacks and network scanning.
Aluminium in Biological Environments: A Computational Approach
Mujika, Jon I; Rezabal, Elixabete; Mercero, Jose M; Ruipérez, Fernando; Costa, Dominique; Ugalde, Jesus M; Lopez, Xabier
2014-01-01
The increased availability of aluminium in biological environments, due to human intervention in the last century, raises concerns on the effects that this so far “excluded from biology” metal might have on living organisms. Consequently, the bioinorganic chemistry of aluminium has emerged as a very active field of research. This review will focus on our contributions to this field, based on computational studies that can yield an understanding of the aluminum biochemistry at a molecular level. Aluminium can interact and be stabilized in biological environments by complexing with both low molecular mass chelants and high molecular mass peptides. The speciation of the metal is, nonetheless, dictated by the hydrolytic species dominant in each case and which vary according to the pH condition of the medium. In blood, citrate and serum transferrin are identified as the main low molecular mass and high molecular mass molecules interacting with aluminium. The complexation of aluminium to citrate and the subsequent changes exerted on the deprotonation pathways of its tritable groups will be discussed along with the mechanisms for the intake and release of aluminium in serum transferrin at two pH conditions, physiological neutral and endosomatic acidic. Aluminium can substitute other metals, in particular magnesium, in protein buried sites and trigger conformational disorder and alteration of the protonation states of the protein's sidechains. A detailed account of the interaction of aluminium with proteic sidechains will be given. Finally, it will be described how alumnium can exert oxidative stress by stabilizing superoxide radicals either as mononuclear aluminium or clustered in boehmite. The possibility of promotion of Fenton reaction, and production of hydroxyl radicals will also be discussed. PMID:24757505
Mutations that Cause Human Disease: A Computational/Experimental Approach
Beernink, P; Barsky, D; Pesavento, B
2006-01-11
International genome sequencing projects have produced billions of nucleotides (letters) of DNA sequence data, including the complete genome sequences of 74 organisms. These genome sequences have created many new scientific opportunities, including the ability to identify sequence variations among individuals within a species. These genetic differences, which are known as single nucleotide polymorphisms (SNPs), are particularly important in understanding the genetic basis for disease susceptibility. Since the report of the complete human genome sequence, over two million human SNPs have been identified, including a large-scale comparison of an entire chromosome from twenty individuals. Of the protein coding SNPs (cSNPs), approximately half leads to a single amino acid change in the encoded protein (non-synonymous coding SNPs). Most of these changes are functionally silent, while the remainder negatively impact the protein and sometimes cause human disease. To date, over 550 SNPs have been found to cause single locus (monogenic) diseases and many others have been associated with polygenic diseases. SNPs have been linked to specific human diseases, including late-onset Parkinson disease, autism, rheumatoid arthritis and cancer. The ability to predict accurately the effects of these SNPs on protein function would represent a major advance toward understanding these diseases. To date several attempts have been made toward predicting the effects of such mutations. The most successful of these is a computational approach called ''Sorting Intolerant From Tolerant'' (SIFT). This method uses sequence conservation among many similar proteins to predict which residues in a protein are functionally important. However, this method suffers from several limitations. First, a query sequence must have a sufficient number of relatives to infer sequence conservation. Second, this method does not make use of or provide any information on protein structure, which can be used to
A Process Education Approach To Teaching Computer Science.
ERIC Educational Resources Information Center
Smith, Peter D.
The driving force of process education is its focus on students'"learning to learn." This paper describes an approach to teaching computer science which includes classroom management; the adaptation of four different courses to follow the process education approach; successes achieved; and students' responses. The courses are conducted in closed…
Estrada, T; Zhang, B; Cicotti, P; Armen, R S; Taufer, M
2012-07-01
We present a scalable and accurate method for classifying protein-ligand binding geometries in molecular docking. Our method is a three-step process: the first step encodes the geometry of a three-dimensional (3D) ligand conformation into a single 3D point in the space; the second step builds an octree by assigning an octant identifier to every single point in the space under consideration; and the third step performs an octree-based clustering on the reduced conformation space and identifies the most dense octant. We adapt our method for MapReduce and implement it in Hadoop. The load-balancing, fault-tolerance, and scalability in MapReduce allow screening of very large conformation spaces not approachable with traditional clustering methods. We analyze results for docking trials for 23 protein-ligand complexes for HIV protease, 21 protein-ligand complexes for Trypsin, and 12 protein-ligand complexes for P38alpha kinase. We also analyze cross docking trials for 24 ligands, each docking into 24 protein conformations of the HIV protease, and receptor ensemble docking trials for 24 ligands, each docking in a pool of HIV protease receptors. Our method demonstrates significant improvement over energy-only scoring for the accurate identification of native ligand geometries in all these docking assessments. The advantages of our clustering approach make it attractive for complex applications in real-world drug design efforts. We demonstrate that our method is particularly useful for clustering docking results using a minimal ensemble of representative protein conformational states (receptor ensemble docking), which is now a common strategy to address protein flexibility in molecular docking. PMID:22658682
NASA Astrophysics Data System (ADS)
Gan, Chenquan; Yang, Xiaofan; Liu, Wanping; Zhu, Qingyi; Jin, Jian; He, Li
2014-08-01
Based on the assumption that external computers (particularly, infected external computers) are connected to the Internet, and by considering the influence of the Internet topology on computer virus spreading, this paper establishes a novel computer virus propagation model with a complex-network approach. This model possesses a unique (viral) equilibrium which is globally attractive. Some numerical simulations are also given to illustrate this result. Further study shows that the computers with higher node degrees are more susceptible to infection than those with lower node degrees. In this regard, some appropriate protective measures are suggested.
Immonen, Taina; Gibson, Richard; Leitner, Thomas; Miller, Melanie A; Arts, Eric J; Somersalo, Erkki; Calvetti, Daniela
2012-11-01
We present a new hybrid stochastic-deterministic, spatially distributed computational model to simulate growth competition assays on a relatively immobile monolayer of peripheral blood mononuclear cells (PBMCs), commonly used for determining ex vivo fitness of human immunodeficiency virus type-1 (HIV-1). The novel features of our approach include incorporation of viral diffusion through a deterministic diffusion model while simulating cellular dynamics via a stochastic Markov chain model. The model accounts for multiple infections of target cells, CD4-downregulation, and the delay between the infection of a cell and the production of new virus particles. The minimum threshold level of infection induced by a virus inoculum is determined via a series of dilution experiments, and is used to determine the probability of infection of a susceptible cell as a function of local virus density. We illustrate how this model can be used for estimating the distribution of cells infected by either a single virus type or two competing viruses. Our model captures experimentally observed variation in the fitness difference between two virus strains, and suggests a way to minimize variation and dual infection in experiments.
NASA Astrophysics Data System (ADS)
McMillin, L. M.; Crone, L. J.; Goldberg, M. D.; Kleespies, T. J.
1995-09-01
A fast and accurate method for the generation of atmospheric transmittances, optical path transmittance (OPTRAN), is described. Results from OPTRAN are compared with those produced by other currently used methods. OPTRAN produces transmittances that can be used to generate brightness temperatures that are accurate to better than 0.2 K, well over 10 times as accurate as the current methods. This is significant because it brings the accuracy of transmittance computation to a level at which it will not adversely affect atmospheric retrievals. OPTRAN is the product of an evolution of approaches developed earlier at the National Environmental Satellite, Data, and Information Service. A majorfeature of OPTRAN that contributes to its accuracy is that transmittance is obtained as a function of the absorber amount rather than the pressure.
Wang, Jing; Xing, Lei
2010-01-01
The presence of metals in patients causes streaking artifacts in X-ray CT and has been recognized as a problem that limits various applications of CT imaging. Accurate localization of metals in CT images is a critical step for metal artifacts reduction in CT imaging and many practical applications of CT images. The purpose of this work is to develop a method of auto-determination of the shape and location of metallic object(s) in the image space. The proposed method is based on the fact that when a metal object is present in a patient, a CT image can be divided into two prominent components: high density metal and low density normal tissues. This prior knowledge is incorporated into an objective function as the regularization term whose role is to encourage the solution to take a form of two intensity levels. A computer simulation study and four experimental studies are performed to evaluate the proposed approach. Both simulation and experimental studies show that the presented algorithm works well even in the presence of complicated shaped metal objects. For a hexagonally shaped metal embedded in a water phantom, for example, it is found that the accuracy of metal reconstruction is within sub-millimeter.
Li, Qiang; Zhang, Wei; Guan, Xin; Bai, Yu; Jia, Jing
2014-01-01
The intima-media thickness (IMT) of common carotid artery (CCA) can serve as an important indicator for the assessment of cardiovascular diseases (CVDs). In this paper an improved approach for automatic IMT measurement with low complexity and high accuracy is presented. 100 ultrasound images from 100 patients were tested with the proposed approach. The ground truth (GT) of the IMT was manually measured for six times and averaged, while the automatic segmented (AS) IMT was computed by the algorithm proposed in this paper. The mean difference ± standard deviation between AS and GT IMT is 0.0231 ± 0.0348 mm, and the correlation coefficient between them is 0.9629. The computational time is 0.3223 s per image with MATLAB under Windows XP on an Intel Core 2 Duo CPU E7500 @2.93 GHz. The proposed algorithm has the potential to achieve real-time measurement under Visual Studio. PMID:25215292
An approach to computing direction relations between separated object groups
NASA Astrophysics Data System (ADS)
Yan, H.; Wang, Z.; Li, J.
2013-06-01
Direction relations between object groups play an important role in qualitative spatial reasoning, spatial computation and spatial recognition. However, none of existing models can be used to compute direction relations between object groups. To fill this gap, an approach to computing direction relations between separated object groups is proposed in this paper, which is theoretically based on Gestalt principles and the idea of multi-directions. The approach firstly triangulates the two object groups; and then it constructs the Voronoi Diagram between the two groups using the triangular network; after this, the normal of each Vornoi edge is calculated, and the quantitative expression of the direction relations is constructed; finally, the quantitative direction relations are transformed into qualitative ones. The psychological experiments show that the proposed approach can obtain direction relations both between two single objects and between two object groups, and the results are correct from the point of view of spatial cognition.
An approach to computing direction relations between separated object groups
NASA Astrophysics Data System (ADS)
Yan, H.; Wang, Z.; Li, J.
2013-09-01
Direction relations between object groups play an important role in qualitative spatial reasoning, spatial computation and spatial recognition. However, none of existing models can be used to compute direction relations between object groups. To fill this gap, an approach to computing direction relations between separated object groups is proposed in this paper, which is theoretically based on gestalt principles and the idea of multi-directions. The approach firstly triangulates the two object groups, and then it constructs the Voronoi diagram between the two groups using the triangular network. After this, the normal of each Voronoi edge is calculated, and the quantitative expression of the direction relations is constructed. Finally, the quantitative direction relations are transformed into qualitative ones. The psychological experiments show that the proposed approach can obtain direction relations both between two single objects and between two object groups, and the results are correct from the point of view of spatial cognition.
A tale of three bio-inspired computational approaches
NASA Astrophysics Data System (ADS)
Schaffer, J. David
2014-05-01
I will provide a high level walk-through for three computational approaches derived from Nature. First, evolutionary computation implements what we may call the "mother of all adaptive processes." Some variants on the basic algorithms will be sketched and some lessons I have gleaned from three decades of working with EC will be covered. Then neural networks, computational approaches that have long been studied as possible ways to make "thinking machines", an old dream of man's, and based upon the only known existing example of intelligence. Then, a little overview of attempts to combine these two approaches that some hope will allow us to evolve machines we could never hand-craft. Finally, I will touch on artificial immune systems, Nature's highly sophisticated defense mechanism, that has emerged in two major stages, the innate and the adaptive immune systems. This technology is finding applications in the cyber security world.
Sensing and perception: Connectionist approaches to subcognitive computing
NASA Technical Reports Server (NTRS)
Skrrypek, J.
1987-01-01
New approaches to machine sensing and perception are presented. The motivation for crossdisciplinary studies of perception in terms of AI and neurosciences is suggested. The question of computing architecture granularity as related to global/local computation underlying perceptual function is considered and examples of two environments are given. Finally, the examples of using one of the environments, UCLA PUNNS, to study neural architectures for visual function are presented.
The process group approach to reliable distributed computing
NASA Technical Reports Server (NTRS)
Birman, Kenneth P.
1992-01-01
The difficulty of developing reliable distribution software is an impediment to applying distributed computing technology in many settings. Experience with the ISIS system suggests that a structured approach based on virtually synchronous process groups yields systems that are substantially easier to develop, exploit sophisticated forms of cooperative computation, and achieve high reliability. Six years of research on ISIS, describing the model, its implementation challenges, and the types of applications to which ISIS has been applied are reviewed.
Singh, Nidhi; Warshel, Arieh
2009-01-01
effectively captures the physics of these entropic effects. The success of the current approach indicates that it should be applicable to the studies of the solvation entropies in the proteins and also, in examining hydrophobic effects. Thus, we believe that the RR approach provides a powerful tool for evaluating the corresponding contributions to the binding entropies and eventually, to the binding free energies. This holds promise for extending the information theory modeling to proteins and protein-ligand complexes in aqueous solutions and consequently, facilitating computer-aided drug design. PMID:19402609
Singh, Nidhi; Warshel, Arieh
2009-05-21
divalent ions and effectively captures the physics of these entropic effects. The success of the current approach indicates that it should be applicable to the studies of the solvation entropies in the proteins and also, in examining hydrophobic effects. Thus, we believe that the RR approach provides a powerful tool for evaluating the corresponding contributions to the binding entropies and, eventually, to the binding free energies. This holds promise for extending the information theory modeling to proteins and protein-ligand complexes in aqueous solutions and consequently, facilitating computer-aided drug design.
NASA Astrophysics Data System (ADS)
Martin, Y. L.
The performance of quantitative analysis of 1D NMR spectra depends greatly on the choice of the NMR signal model. Complex least-squares analysis is well suited for optimizing the quantitative determination of spectra containing a limited number of signals (<30) obtained under satisfactory conditions of signal-to-noise ratio (>20). From a general point of view it is concluded, on the basis of mathematical considerations and numerical simulations, that, in the absence of truncation of the free-induction decay, complex least-squares curve fitting either in the time or in the frequency domain and linear-prediction methods are in fact nearly equivalent and give identical results. However, in the situation considered, complex least-squares analysis in the frequency domain is more flexible since it enables the quality of convergence to be appraised at every resonance position. An efficient data-processing strategy has been developed which makes use of an approximate conjugate-gradient algorithm. All spectral parameters (frequency, damping factors, amplitudes, phases, initial delay associated with intensity, and phase parameters of a baseline correction) are simultaneously managed in an integrated approach which is fully automatable. The behavior of the error as a function of the signal-to-noise ratio is theoretically estimated, and the influence of apodization is discussed. The least-squares curve fitting is theoretically proved to be the most accurate approach for quantitative analysis of 1D NMR data acquired with reasonable signal-to-noise ratio. The method enables complex spectral residuals to be sorted out. These residuals, which can be cumulated thanks to the possibility of correcting for frequency shifts and phase errors, extract systematic components, such as isotopic satellite lines, and characterize the shape and the intensity of the spectral distortion with respect to the Lorentzian model. This distortion is shown to be nearly independent of the chemical species
Computational approach to the study of thermal spin crossover phenomena
Rudavskyi, Andrii; Broer, Ria; Sousa, Carmen
2014-05-14
The key parameters associated to the thermally induced spin crossover process have been calculated for a series of Fe(II) complexes with mono-, bi-, and tridentate ligands. Combination of density functional theory calculations for the geometries and for normal vibrational modes, and highly correlated wave function methods for the energies, allows us to accurately compute the entropy variation associated to the spin transition and the zero-point corrected energy difference between the low- and high-spin states. From these values, the transition temperature, T{sub 1/2}, is estimated for different compounds.
Jung, Hee-Jung; Purvine, Samuel O.; Kim, Hokeun; Petyuk, Vladislav A.; Hyung, Seok-Won; Monroe, Matthew E.; Mun, Dong-Gi; Kim, Kyong-Chul; Park, Jong-Moon; Kim, Su-Jin; Tolic, Nikola; Slysz, Gordon W.; Moore, Ronald J.; Zhao, Rui; Adkins, Joshua N.; Anderson, Gordon A.; Lee, Hookeun; Camp, David G.; Yu, Myeong-Hee; Smith, Richard D.; Lee, Sang-Won
2010-01-01
Accurate assignment of monoisotopic precursor masses to tandem mass spectrometric (MS/MS) data is a fundamental and critically important step for successful peptide identifications in mass spectrometry based proteomics. Here we describe an integrated approach that combines three previously reported methods of treating MS/MS data for precursor mass refinement. This combined method, “integrated Post-Experiment Monoisotopic Mass Refinement” (iPE-MMR), integrates steps: 1) generation of refined MS/MS data by DeconMSn; 2) additional refinement of the resultant MS/MS data by a modified version of PE-MMR; 3) elimination of systematic errors of precursor masses using DtaRefinery. iPE-MMR is the first method that utilizes all MS information from multiple MS scans of a precursor ion including multiple charge states, in an MS scan, to determine precursor mass. By combining these methods, iPE-MMR increases sensitivity in peptide identification and provides increased accuracy when applied to complex high-throughput proteomics data. PMID:20863060
A Computationally Based Approach to Homogenizing Advanced Alloys
Jablonski, P D; Cowen, C J
2011-02-27
We have developed a computationally based approach to optimizing the homogenization heat treatment of complex alloys. The Scheil module within the Thermo-Calc software is used to predict the as-cast segregation present within alloys, and DICTRA (Diffusion Controlled TRAnsformations) is used to model the homogenization kinetics as a function of time, temperature and microstructural scale. We will discuss this approach as it is applied to both Ni based superalloys as well as the more complex (computationally) case of alloys that solidify with more than one matrix phase as a result of segregation. Such is the case typically observed in martensitic steels. With these alloys it is doubly important to homogenize them correctly, especially at the laboratory scale, since they are austenitic at high temperature and thus constituent elements will diffuse slowly. The computationally designed heat treatment and the subsequent verification real castings are presented.
Time-Accurate, Unstructured-Mesh Navier-Stokes Computations with the Space-Time CESE Method
NASA Technical Reports Server (NTRS)
Chang, Chau-Lyan
2006-01-01
Application of the newly emerged space-time conservation element solution element (CESE) method to compressible Navier-Stokes equations is studied. In contrast to Euler equations solvers, several issues such as boundary conditions, numerical dissipation, and grid stiffness warrant systematic investigations and validations. Non-reflecting boundary conditions applied at the truncated boundary are also investigated from the stand point of acoustic wave propagation. Validations of the numerical solutions are performed by comparing with exact solutions for steady-state as well as time-accurate viscous flow problems. The test cases cover a broad speed regime for problems ranging from acoustic wave propagation to 3D hypersonic configurations. Model problems pertinent to hypersonic configurations demonstrate the effectiveness of the CESE method in treating flows with shocks, unsteady waves, and separations. Good agreement with exact solutions suggests that the space-time CESE method provides a viable alternative for time-accurate Navier-Stokes calculations of a broad range of problems.
Computing solvent-induced forces in the solvation approach called Semi Explicit Assembly
NASA Astrophysics Data System (ADS)
Brini, Emiliano; Hummel, Michelle H.; Coutsias, Evangelos A.; Fennell, Christopher J.; Dill, Ken A.
2014-03-01
Many biologically relevant processes (e.g. protein folding) are often too big and slow to be simulated by computer methods that model atomically detailed water. Faster physical models of water are needed. We have developed an approach called Semi Explicit Assembly (SEA) [C.J. Fennell, C.W. Kehoe, K.A. Dill, PNAS, 108, 3234 (2011)]. It is physical because it uses pre-simulations of explicit-solvent models, and it is fast because at runtime, we just combine the pre-simulated results in rapid computations. SEA has also now been proven physically accurate in two blind tests called SAMPL. Here, we describe the computation of solvation forces in SEA, so that this solvation procedure can be incorporated into standard molecular dynamics codes. We describe experimental tests.
Zheng, Yefeng; Tek, Huseyin; Funka-Lea, Gareth
2013-01-01
Various methods have been proposed to extract coronary artery centerlines from computed tomography angiography (CTA) data. Almost all previous approaches are data-driven, which try to trace a centerline from an automatically detected or manually specified coronary ostium. No or little high level prior information is used; therefore, the centerline tracing procedure may terminate early at a severe occlusion or an anatomically inconsistent centerline course may be generated. Though the connectivity of coronary arteries exhibits large variations, the position of major coronary arteries relative to the heart chambers is quite stable. In this work, we propose to exploit the automatically segmented chambers to 1) predict the initial position of the major coronary centerlines and 2) define a vessel-specific region-of-interest (ROI) to constrain the following centerline refinement. The proposed prior constraints have been integrated into a model-driven algorithm for the extraction of three major coronary centerlines, namely the left anterior descending artery (LAD), left circumflex artery (LCX), and right coronary artery (RCA). After extracting the major coronary arteries, the side branches are traced using a data-driven approach to handle large anatomical variations in side branches. Experiments on the public Rotterdam coronary CTA database demonstrate the robustness and accuracy of the proposed method. We achieve the best average ranking on overlap metrics among automatic methods and our accuracy metric outperforms all other 22 methods (including both automatic and semi-automatic methods). PMID:24505746
An engineering based approach for hydraulic computations in river flows
NASA Astrophysics Data System (ADS)
Di Francesco, S.; Biscarini, C.; Pierleoni, A.; Manciola, P.
2016-06-01
This paper presents an engineering based approach for hydraulic risk evaluation. The aim of the research is to identify a criteria for the choice of the simplest and appropriate model to use in different scenarios varying the characteristics of main river channel. The complete flow field, generally expressed in terms of pressure, velocities, accelerations can be described through a three dimensional approach that consider all the flow properties varying in all directions. In many practical applications for river flow studies, however, the greatest changes occur only in two dimensions or even only in one. In these cases the use of simplified approaches can lead to accurate results, with easy to build and faster simulations. The study has been conducted taking in account a dimensionless parameter of channels (ratio of curvature radius and width of the channel (R/B).
Cloud computing approaches to accelerate drug discovery value chain.
Garg, Vibhav; Arora, Suchir; Gupta, Chitra
2011-12-01
Continued advancements in the area of technology have helped high throughput screening (HTS) evolve from a linear to parallel approach by performing system level screening. Advanced experimental methods used for HTS at various steps of drug discovery (i.e. target identification, target validation, lead identification and lead validation) can generate data of the order of terabytes. As a consequence, there is pressing need to store, manage, mine and analyze this data to identify informational tags. This need is again posing challenges to computer scientists to offer the matching hardware and software infrastructure, while managing the varying degree of desired computational power. Therefore, the potential of "On-Demand Hardware" and "Software as a Service (SAAS)" delivery mechanisms cannot be denied. This on-demand computing, largely referred to as Cloud Computing, is now transforming the drug discovery research. Also, integration of Cloud computing with parallel computing is certainly expanding its footprint in the life sciences community. The speed, efficiency and cost effectiveness have made cloud computing a 'good to have tool' for researchers, providing them significant flexibility, allowing them to focus on the 'what' of science and not the 'how'. Once reached to its maturity, Discovery-Cloud would fit best to manage drug discovery and clinical development data, generated using advanced HTS techniques, hence supporting the vision of personalized medicine.
O’Kane, Dermot B.; Lawrentschuk, Nathan; Bolton, Damien M.
2016-01-01
We herein present a case of a 76-year-old gentleman, where prostate-specific membrane antigen positron emission tomography-computed tomography (PSMA PET-CT) was used to accurately detect prostate cancer (PCa), pelvic lymph node (LN) metastasis in the setting of biochemical recurrence following definitive treatment for PCa. The positive PSMA PET-CT result was confirmed with histological examination of the involved pelvic LNs following pelvic LN dissection. PMID:27141207
NASA Astrophysics Data System (ADS)
Shi, Guangyuan; Li, Song; Huang, Ke; Li, Zile; Zheng, Guoxing
2016-10-01
We have developed a new numerical ray-tracing approach for LIDAR signal power function computation, in which the light round-trip propagation is analyzed by geometrical optics and a simple experiment is employed to acquire the laser intensity distribution. It is relatively more accurate and flexible than previous methods. We emphatically discuss the relationship between the inclined angle and the dynamic range of detector output signal in biaxial LIDAR system. Results indicate that an appropriate negative angle can compress the signal dynamic range. This technique has been successfully proved by comparison with real measurements.
NASA Astrophysics Data System (ADS)
Shi, Guangyuan; Li, Song; Huang, Ke; Li, Zile; Zheng, Guoxing
2016-08-01
We have developed a new numerical ray-tracing approach for LIDAR signal power function computation, in which the light round-trip propagation is analyzed by geometrical optics and a simple experiment is employed to acquire the laser intensity distribution. It is relatively more accurate and flexible than previous methods. We emphatically discuss the relationship between the inclined angle and the dynamic range of detector output signal in biaxial LIDAR system. Results indicate that an appropriate negative angle can compress the signal dynamic range. This technique has been successfully proved by comparison with real measurements.
Fragment-based approaches and computer-aided drug discovery.
Rognan, Didier
2012-01-01
Fragment-based design has significantly modified drug discovery strategies and paradigms in the last decade. Besides technological advances and novel therapeutic avenues, one of the most significant changes brought by this new discipline has occurred in the minds of drug designers. Fragment-based approaches have markedly impacted rational computer-aided design both in method development and in applications. The present review illustrates the importance of molecular fragments in many aspects of rational ligand design, and discusses how thinking in "fragment space" has boosted computational biology and chemistry. PMID:21710380
One approach for evaluating the Distributed Computing Design System (DCDS)
NASA Technical Reports Server (NTRS)
Ellis, J. T.
1985-01-01
The Distributed Computer Design System (DCDS) provides an integrated environment to support the life cycle of developing real-time distributed computing systems. The primary focus of DCDS is to significantly increase system reliability and software development productivity, and to minimize schedule and cost risk. DCDS consists of integrated methodologies, languages, and tools to support the life cycle of developing distributed software and systems. Smooth and well-defined transistions from phase to phase, language to language, and tool to tool provide a unique and unified environment. An approach to evaluating DCDS highlights its benefits.
Sesé, Luis M
2012-06-28
A systematic study of the direct computation of the isothermal compressibility of normal quantum fluids is presented by analyzing the solving of the Ornstein-Zernike integral (OZ2) equation for the pair correlations between the path-integral necklace centroids. A number of issues related to the accuracy that can be achieved via this sort of procedure have been addressed, paying particular attention to the finite-N effects and to the definition of significant error bars for the estimates of isothermal compressibilities. Extensive path-integral Monte Carlo computations for the quantum hard-sphere fluid (QHS) have been performed in the (N, V, T) ensemble under temperature and density conditions for which dispersion effects dominate the quantum behavior. These computations have served to obtain the centroid correlations, which have been processed further via the numerical solving of the OZ2 equation. To do so, Baxter-Dixon-Hutchinson's variational procedure, complemented with Baumketner-Hiwatari's grand-canonical corrections, has been used. The virial equation of state has also been obtained and several comparisons between different versions of the QHS equation of state have been made. The results show the reliability of the procedure based on isothermal compressibilities discussed herein, which can then be regarded as a useful and quick means of obtaining the equation of state for fluids under quantum conditions involving strong repulsive interactions.
Style: A Computational and Conceptual Blending-Based Approach
NASA Astrophysics Data System (ADS)
Goguen, Joseph A.; Harrell, D. Fox
This chapter proposes a new approach to style, arising from our work on computational media using structural blending, which enriches the conceptual blending of cognitive linguistics with structure building operations in order to encompass syntax and narrative as well as metaphor. We have implemented both conceptual and structural blending, and conducted initial experiments with poetry, including interactive multimedia poetry, although the approach generalizes to other media. The central idea is to generate multimedia content and analyze style in terms of blending principles, based on our finding that different principles from those of common sense blending are often needed for some contemporary poetic metaphors.
Computational approaches for human disease gene prediction and ranking.
Zhu, Cheng; Wu, Chao; Aronow, Bruce J; Jegga, Anil G
2014-01-01
While candidate gene association studies continue to be the most practical and frequently employed approach in disease gene investigation for complex disorders, selecting suitable genes to test is a challenge. There are several computational approaches available for selecting and prioritizing disease candidate genes. A majority of these tools are based on guilt-by-association principle where novel disease candidate genes are identified and prioritized based on either functional or topological similarity to known disease genes. In this chapter we review the prioritization criteria and the algorithms along with some use cases that demonstrate how these tools can be used for identifying and ranking human disease candidate genes.
Computer Synthesis Approaches of Hyperboloid Gear Drives with Linear Contact
NASA Astrophysics Data System (ADS)
Abadjiev, Valentin; Kawasaki, Haruhisa
2014-09-01
The computer design has improved forming different type software for scientific researches in the field of gearing theory as well as performing an adequate scientific support of the gear drives manufacture. Here are attached computer programs that are based on mathematical models as a result of scientific researches. The modern gear transmissions require the construction of new mathematical approaches to their geometric, technological and strength analysis. The process of optimization, synthesis and design is based on adequate iteration procedures to find out an optimal solution by varying definite parameters. The study is dedicated to accepted methodology in the creation of soft- ware for the synthesis of a class high reduction hyperboloid gears - Spiroid and Helicon ones (Spiroid and Helicon are trademarks registered by the Illinois Tool Works, Chicago, Ill). The developed basic computer products belong to software, based on original mathematical models. They are based on the two mathematical models for the synthesis: "upon a pitch contact point" and "upon a mesh region". Computer programs are worked out on the basis of the described mathematical models, and the relations between them are shown. The application of the shown approaches to the synthesis of commented gear drives is illustrated.
Archiving Software Systems: Approaches to Preserve Computational Capabilities
NASA Astrophysics Data System (ADS)
King, T. A.
2014-12-01
A great deal of effort is made to preserve scientific data. Not only because data is knowledge, but it is often costly to acquire and is sometimes collected under unique circumstances. Another part of the science enterprise is the development of software to process and analyze the data. Developed software is also a large investment and worthy of preservation. However, the long term preservation of software presents some challenges. Software often requires a specific technology stack to operate. This can include software, operating systems and hardware dependencies. One past approach to preserve computational capabilities is to maintain ancient hardware long past its typical viability. On an archive horizon of 100 years, this is not feasible. Another approach to preserve computational capabilities is to archive source code. While this can preserve details of the implementation and algorithms, it may not be possible to reproduce the technology stack needed to compile and run the resulting applications. This future forward dilemma has a solution. Technology used to create clouds and process big data can also be used to archive and preserve computational capabilities. We explore how basic hardware, virtual machines, containers and appropriate metadata can be used to preserve computational capabilities and to archive functional software systems. In conjunction with data archives, this provides scientist with both the data and capability to reproduce the processing and analysis used to generate past scientific results.
Novel Approaches to Adaptive Angular Approximations in Computational Transport
Marvin L. Adams; Igor Carron; Paul Nelson
2006-06-04
The particle-transport equation is notoriously difficult to discretize accurately, largely because the solution can be discontinuous in every variable. At any given spatial position and energy E, for example, the transport solution can be discontinuous at an arbitrary number of arbitrary locations in the direction domain. Even if the solution is continuous it is often devoid of smoothness. This makes the direction variable extremely difficult to discretize accurately. We have attacked this problem with adaptive discretizations in the angle variables, using two distinctly different approaches. The first approach used wavelet function expansions directly and exploited their ability to capture sharp local variations. The second used discrete ordinates with a spatially varying quadrature set that adapts to the local solution. The first approach is very different from that in today’s transport codes, while the second could conceivably be implemented in such codes. Both approaches succeed in reducing angular discretization error to any desired level. The work described and results presented in this report add significantly to the understanding of angular discretization in transport problems and demonstrate that it is possible to solve this important long-standing problem in deterministic transport. Our results show that our adaptive discrete-ordinates (ADO) approach successfully: 1) Reduces angular discretization error to user-selected “tolerance” levels in a variety of difficult test problems; 2) Achieves a given error with significantly fewer unknowns than non-adaptive discrete ordinates methods; 3) Can be implemented within standard discrete-ordinates solution techniques, and thus could generate a significant impact on the field in a relatively short time. Our results show that our adaptive wavelet approach: 1) Successfully reduces the angular discretization error to arbitrarily small levels in a variety of difficult test problems, even when using the
The Berlin Brain--Computer Interface: accurate performance from first-session in BCI-naïve subjects.
Blankertz, Benjamin; Losch, Florian; Krauledat, Matthias; Dornhege, Guido; Curio, Gabriel; Müller, Klaus-Robert
2008-10-01
The Berlin Brain--Computer Interface (BBCI) project develops a noninvasive BCI system whose key features are: 1) the use of well-established motor competences as control paradigms; 2) high-dimensional features from multichannel EEG; and 3) advanced machine-learning techniques. Spatio-spectral changes of sensorimotor rhythms are used to discriminate imagined movements (left hand, right hand, and foot). A previous feedback study [M. Krauledat, K.-R. MUller, and G. Curio. (2007) The non-invasive Berlin brain--computer Interface: Fast acquisition of effective performance in untrained subjects. NeuroImage. [Online]. 37(2), pp. 539--550. Available: http://dx.doi.org/10.1016/j.neuroimage.2007.01.051] with ten subjects provided preliminary evidence that the BBCI system can be operated at high accuracy for subjects with less than five prior BCI exposures. Here, we demonstrate in a group of 14 fully BCI-naIve subjects that 8 out of 14 BCI novices can perform at >84% accuracy in their very first BCI session, and a further four subjects at >70%. Thus, 12 out of 14 BCI-novices had significant above-chance level performances without any subject training even in the first session, as based on an optimized EEG analysis by advanced machine-learning algorithms. PMID:18838371
Gritzo, L.A.; Koski, J.A.; Suo-Anttila, A.J.
1999-03-16
The Container Analysis Fire Environment computer code (CAFE) is intended to provide Type B package designers with an enhanced engulfing fire boundary condition when combined with the PATRAN/P-Thermal commercial code. Historically an engulfing fire boundary condition has been modeled as {sigma}T{sup 4} where {sigma} is the Stefan-Boltzman constant, and T is the fire temperature. The CAFE code includes the necessary chemistry, thermal radiation, and fluid mechanics to model an engulfing fire. Effects included are the local cooling of gases that form a protective boundary layer that reduces the incoming radiant heat flux to values lower than expected from a simple {sigma}T{sup 4} model. In addition, the effect of object shape on mixing that may increase the local fire temperature is included. Both high and low temperature regions that depend upon the local availability of oxygen are also calculated. Thus the competing effects that can both increase and decrease the local values of radiant heat flux are included in a reamer that is not predictable a-priori. The CAFE package consists of a group of computer subroutines that can be linked to workstation-based thermal analysis codes in order to predict package performance during regulatory and other accident fire scenarios.
Probabilistic Damage Characterization Using the Computationally-Efficient Bayesian Approach
NASA Technical Reports Server (NTRS)
Warner, James E.; Hochhalter, Jacob D.
2016-01-01
This work presents a computationally-ecient approach for damage determination that quanti es uncertainty in the provided diagnosis. Given strain sensor data that are polluted with measurement errors, Bayesian inference is used to estimate the location, size, and orientation of damage. This approach uses Bayes' Theorem to combine any prior knowledge an analyst may have about the nature of the damage with information provided implicitly by the strain sensor data to form a posterior probability distribution over possible damage states. The unknown damage parameters are then estimated based on samples drawn numerically from this distribution using a Markov Chain Monte Carlo (MCMC) sampling algorithm. Several modi cations are made to the traditional Bayesian inference approach to provide signi cant computational speedup. First, an ecient surrogate model is constructed using sparse grid interpolation to replace a costly nite element model that must otherwise be evaluated for each sample drawn with MCMC. Next, the standard Bayesian posterior distribution is modi ed using a weighted likelihood formulation, which is shown to improve the convergence of the sampling process. Finally, a robust MCMC algorithm, Delayed Rejection Adaptive Metropolis (DRAM), is adopted to sample the probability distribution more eciently. Numerical examples demonstrate that the proposed framework e ectively provides damage estimates with uncertainty quanti cation and can yield orders of magnitude speedup over standard Bayesian approaches.
Alecu, I M; Truhlar, Donald G
2011-04-01
The reactions of CH(3)OH with the HO(2) and CH(3) radicals are important in the combustion of methanol and are prototypes for reactions of heavier alcohols in biofuels. The reaction energies and barrier heights for these reaction systems are computed with CCSD(T) theory extrapolated to the complete basis set limit using correlation-consistent basis sets, both augmented and unaugmented, and further refined by including a fully coupled treatment of the connected triple excitations, a second-order perturbative treatment of quadruple excitations (by CCSDT(2)(Q)), core-valence corrections, and scalar relativistic effects. It is shown that the M08-HX and M08-SO hybrid meta-GGA density functionals can achieve sub-kcal mol(-1) agreement with the high-level ab initio results, identifying these functionals as important potential candidates for direct dynamics studies on the rates of these and homologous reaction systems. PMID:21405059
A simple grand canonical approach to compute the vapor pressure of bulk and finite size systems
Factorovich, Matías H.; Scherlis, Damián A.
2014-02-14
In this article we introduce a simple grand canonical screening (GCS) approach to accurately compute vapor pressures from molecular dynamics or Monte Carlo simulations. This procedure entails a screening of chemical potentials using a conventional grand canonical scheme, and therefore it is straightforward to implement for any kind of interface. The scheme is validated against data obtained from Gibbs ensemble simulations for water and argon. Then, it is applied to obtain the vapor pressure of the coarse-grained mW water model, and it is shown that the computed value is in excellent accord with the one formally deduced using statistical thermodynamics arguments. Finally, this methodology is used to calculate the vapor pressure of a water nanodroplet of 94 molecules. Interestingly, the result is in perfect agreement with the one predicted by the Kelvin equation for a homogeneous droplet of that size.
A simple grand canonical approach to compute the vapor pressure of bulk and finite size systems.
Factorovich, Matías H; Molinero, Valeria; Scherlis, Damián A
2014-02-14
In this article we introduce a simple grand canonical screening (GCS) approach to accurately compute vapor pressures from molecular dynamics or Monte Carlo simulations. This procedure entails a screening of chemical potentials using a conventional grand canonical scheme, and therefore it is straightforward to implement for any kind of interface. The scheme is validated against data obtained from Gibbs ensemble simulations for water and argon. Then, it is applied to obtain the vapor pressure of the coarse-grained mW water model, and it is shown that the computed value is in excellent accord with the one formally deduced using statistical thermodynamics arguments. Finally, this methodology is used to calculate the vapor pressure of a water nanodroplet of 94 molecules. Interestingly, the result is in perfect agreement with the one predicted by the Kelvin equation for a homogeneous droplet of that size.
Sundaramurthy, Aravind; Alai, Aaron; Ganpule, Shailesh; Holmberg, Aaron; Plougonven, Erwan; Chandra, Namas
2012-09-01
Blast waves generated by improvised explosive devices (IEDs) cause traumatic brain injury (TBI) in soldiers and civilians. In vivo animal models that use shock tubes are extensively used in laboratories to simulate field conditions, to identify mechanisms of injury, and to develop injury thresholds. In this article, we place rats in different locations along the length of the shock tube (i.e., inside, outside, and near the exit), to examine the role of animal placement location (APL) in the biomechanical load experienced by the animal. We found that the biomechanical load on the brain and internal organs in the thoracic cavity (lungs and heart) varied significantly depending on the APL. When the specimen is positioned outside, organs in the thoracic cavity experience a higher pressure for a longer duration, in contrast to APL inside the shock tube. This in turn will possibly alter the injury type, severity, and lethality. We found that the optimal APL is where the Friedlander waveform is first formed inside the shock tube. Once the optimal APL was determined, the effect of the incident blast intensity on the surface and intracranial pressure was measured and analyzed. Noticeably, surface and intracranial pressure increases linearly with the incident peak overpressures, though surface pressures are significantly higher than the other two. Further, we developed and validated an anatomically accurate finite element model of the rat head. With this model, we determined that the main pathway of pressure transmission to the brain was through the skull and not through the snout; however, the snout plays a secondary role in diffracting the incoming blast wave towards the skull.
Sundaramurthy, Aravind; Alai, Aaron; Ganpule, Shailesh; Holmberg, Aaron; Plougonven, Erwan; Chandra, Namas
2012-09-01
Blast waves generated by improvised explosive devices (IEDs) cause traumatic brain injury (TBI) in soldiers and civilians. In vivo animal models that use shock tubes are extensively used in laboratories to simulate field conditions, to identify mechanisms of injury, and to develop injury thresholds. In this article, we place rats in different locations along the length of the shock tube (i.e., inside, outside, and near the exit), to examine the role of animal placement location (APL) in the biomechanical load experienced by the animal. We found that the biomechanical load on the brain and internal organs in the thoracic cavity (lungs and heart) varied significantly depending on the APL. When the specimen is positioned outside, organs in the thoracic cavity experience a higher pressure for a longer duration, in contrast to APL inside the shock tube. This in turn will possibly alter the injury type, severity, and lethality. We found that the optimal APL is where the Friedlander waveform is first formed inside the shock tube. Once the optimal APL was determined, the effect of the incident blast intensity on the surface and intracranial pressure was measured and analyzed. Noticeably, surface and intracranial pressure increases linearly with the incident peak overpressures, though surface pressures are significantly higher than the other two. Further, we developed and validated an anatomically accurate finite element model of the rat head. With this model, we determined that the main pathway of pressure transmission to the brain was through the skull and not through the snout; however, the snout plays a secondary role in diffracting the incoming blast wave towards the skull. PMID:22620716
A low-computational approach on gaze estimation with eye touch system.
Topal, Cihan; Gunal, Serkan; Koçdeviren, Onur; Doğan, Atakan; Gerek, Ömer Nezih
2014-02-01
Among various approaches to eye tracking systems, light-reflection based systems with non-imaging sensors, e.g., photodiodes or phototransistors, are known to have relatively low complexity; yet, they provide moderately accurate estimation of the point of gaze. In this paper, a low-computational approach on gaze estimation is proposed using the Eye Touch system, which is a light-reflection based eye tracking system, previously introduced by the authors. Based on the physical implementation of Eye Touch, the sensor measurements are now utilized in low-computational least-squares algorithms to estimate arbitrary gaze directions, unlike the existing light reflection-based systems, including the initial Eye Touch implementation, where only limited predefined regions were distinguished. The system also utilizes an effective pattern classification algorithm to be able to perform left, right, and double clicks based on respective eye winks with significantly high accuracy. In order to avoid accuracy problems for sensitive sensor biasing hardware, a robust custom microcontroller-based data acquisition system is developed. Consequently, the physical size and cost of the overall Eye Touch system are considerably reduced while the power efficiency is improved. The results of the experimental analysis over numerous subjects clearly indicate that the proposed eye tracking system can classify eye winks with 98% accuracy, and attain an accurate gaze direction with an average angular error of about 0.93 °. Due to its lightweight structure, competitive accuracy and low-computational requirements relative to video-based eye tracking systems, the proposed system is a promising human-computer interface for both stationary and mobile eye tracking applications.
Computational approaches to parameter estimation and model selection in immunology
NASA Astrophysics Data System (ADS)
Baker, C. T. H.; Bocharov, G. A.; Ford, J. M.; Lumb, P. M.; Norton, S. J.; Paul, C. A. H.; Junt, T.; Krebs, P.; Ludewig, B.
2005-12-01
One of the significant challenges in biomathematics (and other areas of science) is to formulate meaningful mathematical models. Our problem is to decide on a parametrized model which is, in some sense, most likely to represent the information in a set of observed data. In this paper, we illustrate the computational implementation of an information-theoretic approach (associated with a maximum likelihood treatment) to modelling in immunology.The approach is illustrated by modelling LCMV infection using a family of models based on systems of ordinary differential and delay differential equations. The models (which use parameters that have a scientific interpretation) are chosen to fit data arising from experimental studies of virus-cytotoxic T lymphocyte kinetics; the parametrized models that result are arranged in a hierarchy by the computation of Akaike indices. The practical illustration is used to convey more general insight. Because the mathematical equations that comprise the models are solved numerically, the accuracy in the computation has a bearing on the outcome, and we address this and other practical details in our discussion.
Computational approaches to detect allosteric pathways in transmembrane molecular machines.
Stolzenberg, Sebastian; Michino, Mayako; LeVine, Michael V; Weinstein, Harel; Shi, Lei
2016-07-01
Many of the functions of transmembrane proteins involved in signal processing and transduction across the cell membrane are determined by allosteric couplings that propagate the functional effects well beyond the original site of activation. Data gathered from breakthroughs in biochemistry, crystallography, and single molecule fluorescence have established a rich basis of information for the study of molecular mechanisms in the allosteric couplings of such transmembrane proteins. The mechanistic details of these couplings, many of which have therapeutic implications, however, have only become accessible in synergy with molecular modeling and simulations. Here, we review some recent computational approaches that analyze allosteric coupling networks (ACNs) in transmembrane proteins, and in particular the recently developed Protein Interaction Analyzer (PIA) designed to study ACNs in the structural ensembles sampled by molecular dynamics simulations. The power of these computational approaches in interrogating the functional mechanisms of transmembrane proteins is illustrated with selected examples of recent experimental and computational studies pursued synergistically in the investigation of secondary active transporters and GPCRs. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
Computational approaches to phenotyping: high-throughput phenomics.
Lussier, Yves A; Liu, Yang
2007-01-01
The recent completion of the Human Genome Project has made possible a high-throughput "systems approach" for accelerating the elucidation of molecular underpinnings of human diseases, and subsequent derivation of molecular-based strategies to more effectively prevent, diagnose, and treat these diseases. Although altered phenotypes are among the most reliable manifestations of altered gene functions, research using systematic analysis of phenotype relationships to study human biology is still in its infancy. This article focuses on the emerging field of high-throughput phenotyping (HTP) phenomics research, which aims to capitalize on novel high-throughput computation and informatics technology developments to derive genomewide molecular networks of genotype-phenotype associations, or "phenomic associations." The HTP phenomics research field faces the challenge of technological research and development to generate novel tools in computation and informatics that will allow researchers to amass, access, integrate, organize, and manage phenotypic databases across species and enable genomewide analysis to associate phenotypic information with genomic data at different scales of biology. Key state-of-the-art technological advancements critical for HTP phenomics research are covered in this review. In particular, we highlight the power of computational approaches to conduct large-scale phenomics studies.
Geng, Jiun-Hung; Tu, Hung-Pin; Shih, Paul Ming-Chen; Shen, Jung-Tsung; Jang, Mei-Yu; Wu, Wen-Jen; Li, Ching-Chia; Chou, Yii-Her; Juan, Yung-Shun
2015-01-01
Urolithiasis is a common disease of the urinary system. Extracorporeal shockwave lithotripsy (SWL) has become one of the standard treatments for renal and ureteral stones; however, the success rates range widely and failure of stone disintegration may cause additional outlay, alternative procedures, and even complications. We used the data available from noncontrast abdominal computed tomography (NCCT) to evaluate the impact of stone parameters and abdominal fat distribution on calculus-free rates following SWL. We retrospectively reviewed 328 patients who had urinary stones and had undergone SWL from August 2012 to August 2013. All of them received pre-SWL NCCT; 1 month after SWL, radiography was arranged to evaluate the condition of the fragments. These patients were classified into stone-free group and residual stone group. Unenhanced computed tomography variables, including stone attenuation, abdominal fat area, and skin-to-stone distance (SSD) were analyzed. In all, 197 (60%) were classified as stone-free and 132 (40%) as having residual stone. The mean ages were 49.35 ± 13.22 years and 55.32 ± 13.52 years, respectively. On univariate analysis, age, stone size, stone surface area, stone attenuation, SSD, total fat area (TFA), abdominal circumference, serum creatinine, and the severity of hydronephrosis revealed statistical significance between these two groups. From multivariate logistic regression analysis, the independent parameters impacting SWL outcomes were stone size, stone attenuation, TFA, and serum creatinine. [Adjusted odds ratios and (95% confidence intervals): 9.49 (3.72-24.20), 2.25 (1.22-4.14), 2.20 (1.10-4.40), and 2.89 (1.35-6.21) respectively, all p < 0.05]. In the present study, stone size, stone attenuation, TFA and serum creatinine were four independent predictors for stone-free rates after SWL. These findings suggest that pretreatment NCCT may predict the outcomes after SWL. Consequently, we can use these predictors for selecting
Alecu, I. M.; Truhlar, D. G.
2011-04-07
The reactions of CH_{3}OH with the HO_{2} and CH_{3} radicals are important in the combustion of methanol and are prototypes for reactions of heavier alcohols in biofuels. The reaction energies and barrier heights for these reaction systems are computed with CCSD(T) theory extrapolated to the complete basis set limit using correlation-consistent basis sets, both augmented and unaugmented, and further refined by including a fully coupled treatment of the connected triple excitations, a second-order perturbative treatment of quadruple excitations (by CCSDT(2)_{Q}), core–valence corrections, and scalar relativistic effects. It is shown that the M08-HX and M08-SO hybrid meta-GGA density functionals can achieve sub-kcal mol^{-1} agreement with the high-level ab initio results, identifying these functionals as important potential candidates for direct dynamics studies on the rates of these and homologous reaction systems.
Hong, Sung-Jin; Her, Ae-Young; Suh, Yongsung; Won, Hoyoun; Cho, Deok-Kyu; Cho, Yun-Hyeong; Yoon, Young-Won; Lee, Kyounghoon; Kang, Woong Chol; Kim, Yong Hoon; Kim, Sang-Wook; Shin, Dong-Ho; Kim, Jung-Sun; Kim, Byeong-Keuk; Ko, Young-Guk; Choi, Byoung-Wook; Choi, Donghoon; Jang, Yangsoo
2016-01-01
Purpose To evaluate the ability of coronary computed tomographic angiography (CCTA) to predict the need of coronary revascularization in symptomatic patients with stable angina who were referred to a cardiac catheterization laboratory for coronary revascularization. Materials and Methods Pre-angiography CCTA findings were analyzed in 1846 consecutive symptomatic patients with stable angina, who were referred to a cardiac catheterization laboratory at six hospitals and were potential candidates for coronary revascularization between July 2011 and December 2013. The number of patients requiring revascularization was determined based on the severity of coronary stenosis as assessed by CCTA. This was compared to the actual number of revascularization procedures performed in the cardiac catheterization laboratory. Results Based on CCTA findings, coronary revascularization was indicated in 877 (48%) and not indicated in 969 (52%) patients. Of the 877 patients indicated for revascularization by CCTA, only 600 (68%) underwent the procedure, whereas 285 (29%) of the 969 patients not indicated for revascularization, as assessed by CCTA, underwent the procedure. When the coronary arteries were divided into 15 segments using the American Heart Association coronary tree model, the sensitivity, specificity, positive predictive value, and negative predictive value of CCTA for therapeutic decision making on a per-segment analysis were 42%, 96%, 40%, and 96%, respectively. Conclusion CCTA-based assessment of coronary stenosis severity does not sufficiently differentiate between coronary segments requiring revascularization versus those not requiring revascularization. Conventional coronary angiography should be considered to determine the need of revascularization in symptomatic patients with stable angina. PMID:27401637
Bedogni, Alberto; Fedele, Stefano; Bedogni, Giorgio; Scoletta, Matteo; Favia, Gianfranco; Colella, Giuseppe; Agrillo, Alessandro; Bettini, Giordana; Di Fede, Olga; Oteri, Giacomo; Fusco, Vittorio; Gabriele, Mario; Ottolenghi, Livia; Valsecchi, Stefano; Porter, Stephen; Petruzzi, Massimo; Arduino, Paolo; D'Amato, Salvatore; Ungari, Claudio; Fung Polly, Pok-Lam; Saia, Giorgia; Campisi, Giuseppina
2014-09-01
Management of osteonecrosis of the jaw associated with antiresorptive agents is challenging, and outcomes are unpredictable. The severity of disease is the main guide to management, and can help to predict prognosis. Most available staging systems for osteonecrosis, including the widely-used American Association of Oral and Maxillofacial Surgeons (AAOMS) system, classify severity on the basis of clinical and radiographic findings. However, clinical inspection and radiography are limited in their ability to identify the extent of necrotic bone disease compared with computed tomography (CT). We have organised a large multicentre retrospective study (known as MISSION) to investigate the agreement between the AAOMS staging system and the extent of osteonecrosis of the jaw (focal compared with diffuse involvement of bone) as detected on CT. We studied 799 patients with detailed clinical phenotyping who had CT images taken. Features of diffuse bone disease were identified on CT within all AAOMS stages (20%, 8%, 48%, and 24% of patients in stages 0, 1, 2, and 3, respectively). Of the patients classified as stage 0, 110/192 (57%) had diffuse disease on CT, and about 1 in 3 with CT evidence of diffuse bone disease was misclassified by the AAOMS system as having stages 0 and 1 osteonecrosis. In addition, more than a third of patients with AAOMS stage 2 (142/405, 35%) had focal bone disease on CT. We conclude that the AAOMS staging system does not correctly identify the extent of bony disease in patients with osteonecrosis of the jaw.
A GPU-COMPUTING APPROACH TO SOLAR STOKES PROFILE INVERSION
Harker, Brian J.; Mighell, Kenneth J. E-mail: mighell@noao.edu
2012-09-20
We present a new computational approach to the inversion of solar photospheric Stokes polarization profiles, under the Milne-Eddington model, for vector magnetography. Our code, named GENESIS, employs multi-threaded parallel-processing techniques to harness the computing power of graphics processing units (GPUs), along with algorithms designed to exploit the inherent parallelism of the Stokes inversion problem. Using a genetic algorithm (GA) engineered specifically for use with a GPU, we produce full-disk maps of the photospheric vector magnetic field from polarized spectral line observations recorded by the Synoptic Optical Long-term Investigations of the Sun (SOLIS) Vector Spectromagnetograph (VSM) instrument. We show the advantages of pairing a population-parallel GA with data-parallel GPU-computing techniques, and present an overview of the Stokes inversion problem, including a description of our adaptation to the GPU-computing paradigm. Full-disk vector magnetograms derived by this method are shown using SOLIS/VSM data observed on 2008 March 28 at 15:45 UT.
A GPU-computing Approach to Solar Stokes Profile Inversion
NASA Astrophysics Data System (ADS)
Harker, Brian J.; Mighell, Kenneth J.
2012-09-01
We present a new computational approach to the inversion of solar photospheric Stokes polarization profiles, under the Milne-Eddington model, for vector magnetography. Our code, named GENESIS, employs multi-threaded parallel-processing techniques to harness the computing power of graphics processing units (GPUs), along with algorithms designed to exploit the inherent parallelism of the Stokes inversion problem. Using a genetic algorithm (GA) engineered specifically for use with a GPU, we produce full-disk maps of the photospheric vector magnetic field from polarized spectral line observations recorded by the Synoptic Optical Long-term Investigations of the Sun (SOLIS) Vector Spectromagnetograph (VSM) instrument. We show the advantages of pairing a population-parallel GA with data-parallel GPU-computing techniques, and present an overview of the Stokes inversion problem, including a description of our adaptation to the GPU-computing paradigm. Full-disk vector magnetograms derived by this method are shown using SOLIS/VSM data observed on 2008 March 28 at 15:45 UT.
Computational approaches in the design of synthetic receptors - A review.
Cowen, Todd; Karim, Kal; Piletsky, Sergey
2016-09-14
The rational design of molecularly imprinted polymers (MIPs) has been a major contributor to their reputation as "plastic antibodies" - high affinity robust synthetic receptors which can be optimally designed, and produced for a much reduced cost than their biological equivalents. Computational design has become a routine procedure in the production of MIPs, and has led to major advances in functional monomer screening, selection of cross-linker and solvent, optimisation of monomer(s)-template ratio and selectivity analysis. In this review the various computational methods will be discussed with reference to all the published relevant literature since the end of 2013, with each article described by the target molecule, the computational approach applied (whether molecular mechanics/molecular dynamics, semi-empirical quantum mechanics, ab initio quantum mechanics (Hartree-Fock, Møller-Plesset, etc.) or DFT) and the purpose for which they were used. Detailed analysis is given to novel techniques including analysis of polymer binding sites, the use of novel screening programs and simulations of MIP polymerisation reaction. The further advances in molecular modelling and computational design of synthetic receptors in particular will have serious impact on the future of nanotechnology and biotechnology, permitting the further translation of MIPs into the realms of analytics and medical technology. PMID:27566340
Computing electronic structures: A new multiconfiguration approach for excited states
Cances, Eric . E-mail: cances@cermics.enpc.fr; Galicher, Herve . E-mail: galicher@cermics.enpc.fr; Lewin, Mathieu . E-mail: lewin@cermic.enpc.fr
2006-02-10
We present a new method for the computation of electronic excited states of molecular systems. This method is based upon a recent theoretical definition of multiconfiguration excited states [due to one of us, see M. Lewin, Solutions of the multiconfiguration equations in quantum chemistry, Arch. Rat. Mech. Anal. 171 (2004) 83-114]. Our algorithm, dedicated to the computation of the first excited state, always converges to a stationary state of the multiconfiguration model, which can be interpreted as an approximate excited state of the molecule. The definition of this approximate excited state is variational. An interesting feature is that it satisfies a non-linear Hylleraas-Undheim-MacDonald type principle: the energy of the approximate excited state is an upper bound to the true excited state energy of the N-body Hamiltonian. To compute the first excited state, one has to deform paths on a manifold, like this is usually done in the search for transition states between reactants and products on potential energy surfaces. We propose here a general method for the deformation of paths which could also be useful in other settings. We also compare our method to other approaches used in Quantum Chemistry and give some explanation of the unsatisfactory behaviours which are sometimes observed when using the latter. Numerical results for the special case of two-electron systems are provided: we compute the first singlet excited state potential energy surface of the H {sub 2} molecule.
Thomas, Peter B. M.; Baltrušaitis, Tadas; Robinson, Peter; Vivian, Anthony J.
2016-01-01
Purpose We validate a video-based method of head posture measurement. Methods The Cambridge Face Tracker uses neural networks (constrained local neural fields) to recognize facial features in video. The relative position of these facial features is used to calculate head posture. First, we assess the accuracy of this approach against videos in three research databases where each frame is tagged with a precisely measured head posture. Second, we compare our method to a commercially available mechanical device, the Cervical Range of Motion device: four subjects each adopted 43 distinct head postures that were measured using both methods. Results The Cambridge Face Tracker achieved confident facial recognition in 92% of the approximately 38,000 frames of video from the three databases. The respective mean error in absolute head posture was 3.34°, 3.86°, and 2.81°, with a median error of 1.97°, 2.16°, and 1.96°. The accuracy decreased with more extreme head posture. Comparing The Cambridge Face Tracker to the Cervical Range of Motion Device gave correlation coefficients of 0.99 (P < 0.0001), 0.96 (P < 0.0001), and 0.99 (P < 0.0001) for yaw, pitch, and roll, respectively. Conclusions The Cambridge Face Tracker performs well under real-world conditions and within the range of normally-encountered head posture. It allows useful quantification of head posture in real time or from precaptured video. Its performance is similar to that of a clinically validated mechanical device. It has significant advantages over other approaches in that subjects do not need to wear any apparatus, and it requires only low cost, easy-to-setup consumer electronics. Translational Relevance Noncontact assessment of head posture allows more complete clinical assessment of patients, and could benefit surgical planning in future. PMID:27730008
An alternative approach for computing seismic response with accidental eccentricity
NASA Astrophysics Data System (ADS)
Fan, Xuanhua; Yin, Jiacong; Sun, Shuli; Chen, Pu
2014-09-01
Accidental eccentricity is a non-standard assumption for seismic design of tall buildings. Taking it into consideration requires reanalysis of seismic resistance, which requires either time consuming computation of natural vibration of eccentric structures or finding a static displacement solution by applying an approximated equivalent torsional moment for each eccentric case. This study proposes an alternative modal response spectrum analysis (MRSA) approach to calculate seismic responses with accidental eccentricity. The proposed approach, called the Rayleigh Ritz Projection-MRSA (RRP-MRSA), is developed based on MRSA and two strategies: (a) a RRP method to obtain a fast calculation of approximate modes of eccentric structures; and (b) an approach to assemble mass matrices of eccentric structures. The efficiency of RRP-MRSA is tested via engineering examples and compared with the standard MRSA (ST-MRSA) and one approximate method, i.e., the equivalent torsional moment hybrid MRSA (ETM-MRSA). Numerical results show that RRP-MRSA not only achieves almost the same precision as ST-MRSA, and is much better than ETM-MRSA, but is also more economical. Thus, RRP-MRSA can be in place of current accidental eccentricity computations in seismic design.
Benchmarking of computer codes and approaches for modeling exposure scenarios
Seitz, R.R.; Rittmann, P.D.; Wood, M.I.; Cook, J.R.
1994-08-01
The US Department of Energy Headquarters established a performance assessment task team (PATT) to integrate the activities of DOE sites that are preparing performance assessments for the disposal of newly generated low-level waste. The PATT chartered a subteam with the task of comparing computer codes and exposure scenarios used for dose calculations in performance assessments. This report documents the efforts of the subteam. Computer codes considered in the comparison include GENII, PATHRAE-EPA, MICROSHIELD, and ISOSHLD. Calculations were also conducted using spreadsheets to provide a comparison at the most fundamental level. Calculations and modeling approaches are compared for unit radionuclide concentrations in water and soil for the ingestion, inhalation, and external dose pathways. Over 30 tables comparing inputs and results are provided.
Computer-based patient record: the essential data set approach.
Moidu, K.; Falsone, J. J.; Nair, S.
1994-01-01
The clamor for data to study the impact of care, to evaluate clinical performance and justify resource utilization is increasing. The data in demand normally should exist in the record of a clinical encounter. Advances in information technology and software techniques have provided us with tools to develop and implement computer-based patient record systems. The issues that constrain development are integral issues of clinical medicine, such as the variability in medical data, specialized practice of medicine, and differing demands of the numerous end-users of a medical record. This paper describes an approach to develop a computer-based patient record. The focus is on identification of the essential data set by infological data modeling and its implementation in a commercially available package for a physician's office. PMID:7949970
Identifying pathogenicity islands in bacterial pathogenomics using computational approaches.
Che, Dongsheng; Hasan, Mohammad Shabbir; Chen, Bernard
2014-01-13
High-throughput sequencing technologies have made it possible to study bacteria through analyzing their genome sequences. For instance, comparative genome sequence analyses can reveal the phenomenon such as gene loss, gene gain, or gene exchange in a genome. By analyzing pathogenic bacterial genomes, we can discover that pathogenic genomic regions in many pathogenic bacteria are horizontally transferred from other bacteria, and these regions are also known as pathogenicity islands (PAIs). PAIs have some detectable properties, such as having different genomic signatures than the rest of the host genomes, and containing mobility genes so that they can be integrated into the host genome. In this review, we will discuss various pathogenicity island-associated features and current computational approaches for the identification of PAIs. Existing pathogenicity island databases and related computational resources will also be discussed, so that researchers may find it to be useful for the studies of bacterial evolution and pathogenicity mechanisms.
Computational approaches for rational design of proteins with novel functionalities.
Tiwari, Manish Kumar; Singh, Ranjitha; Singh, Raushan Kumar; Kim, In-Won; Lee, Jung-Kul
2012-01-01
Proteins are the most multifaceted macromolecules in living systems and have various important functions, including structural, catalytic, sensory, and regulatory functions. Rational design of enzymes is a great challenge to our understanding of protein structure and physical chemistry and has numerous potential applications. Protein design algorithms have been applied to design or engineer proteins that fold, fold faster, catalyze, catalyze faster, signal, and adopt preferred conformational states. The field of de novo protein design, although only a few decades old, is beginning to produce exciting results. Developments in this field are already having a significant impact on biotechnology and chemical biology. The application of powerful computational methods for functional protein designing has recently succeeded at engineering target activities. Here, we review recently reported de novo functional proteins that were developed using various protein design approaches, including rational design, computational optimization, and selection from combinatorial libraries, highlighting recent advances and successes.
A Computational Approach for Probabilistic Analysis of Water Impact Simulations
NASA Technical Reports Server (NTRS)
Horta, Lucas G.; Mason, Brian H.; Lyle, Karen H.
2009-01-01
NASA's development of new concepts for the Crew Exploration Vehicle Orion presents many similar challenges to those worked in the sixties during the Apollo program. However, with improved modeling capabilities, new challenges arise. For example, the use of the commercial code LS-DYNA, although widely used and accepted in the technical community, often involves high-dimensional, time consuming, and computationally intensive simulations. The challenge is to capture what is learned from a limited number of LS-DYNA simulations to develop models that allow users to conduct interpolation of solutions at a fraction of the computational time. This paper presents a description of the LS-DYNA model, a brief summary of the response surface techniques, the analysis of variance approach used in the sensitivity studies, equations used to estimate impact parameters, results showing conditions that might cause injuries, and concluding remarks.
Slide Star: An Approach to Videodisc/Computer Aided Instruction
McEnery, Kevin W.
1984-01-01
One of medical education's primary goals is for the student to be proficient in the gross and microscopic identification of disease. The videodisc, with its storage capacity of up to 54,000 photomicrographs is ideally suited to assist in this educational process. “Slide Star” is a method of interactive instruction which is designed for use in any subject where it is essential to identify visual material. The instructional approach utilizes a computer controlled videodisc to display photomicrographs. In the demonstration program, these are slides of normal blood cells. The program is unique in that the instruction is created by the student's commands manipulating the photomicrograph data base. A prime feature is the use of computer generated multiple choice questions to reinforce the learning process.
Identifying Pathogenicity Islands in Bacterial Pathogenomics Using Computational Approaches
Che, Dongsheng; Hasan, Mohammad Shabbir; Chen, Bernard
2014-01-01
High-throughput sequencing technologies have made it possible to study bacteria through analyzing their genome sequences. For instance, comparative genome sequence analyses can reveal the phenomenon such as gene loss, gene gain, or gene exchange in a genome. By analyzing pathogenic bacterial genomes, we can discover that pathogenic genomic regions in many pathogenic bacteria are horizontally transferred from other bacteria, and these regions are also known as pathogenicity islands (PAIs). PAIs have some detectable properties, such as having different genomic signatures than the rest of the host genomes, and containing mobility genes so that they can be integrated into the host genome. In this review, we will discuss various pathogenicity island-associated features and current computational approaches for the identification of PAIs. Existing pathogenicity island databases and related computational resources will also be discussed, so that researchers may find it to be useful for the studies of bacterial evolution and pathogenicity mechanisms. PMID:25437607
An Efficient Computational Approach for the Calculation of the Vibrational Density of States.
Aieta, Chiara; Gabas, Fabio; Ceotto, Michele
2016-07-14
We present an optimized approach for the calculation of the density of fully coupled vibrational states in high-dimensional systems. This task is of paramount importance, because partition functions and several thermodynamic properties can be accurately estimated once the density of states is known. A new code, called paradensum, based on the implementation of the Wang-Landau Monte Carlo algorithm for parallel architectures is described and applied to real complex systems. We test the accuracy of paradensum on several molecular systems, including some benchmarks for which an exact evaluation of the vibrational density of states is doable by direct counting. In addition, we find a significant computational speedup with respect to standard approaches when applying our code to molecules up to 66 degrees of freedom. The new code can easily handle 150 degrees of freedom. These features make paradensum a very promising tool for future calculations of thermodynamic properties and thermal rate constants of complex systems. PMID:26840098
A pencil beam approach to proton computed tomography
Rescigno, Regina Bopp, Cécile; Rousseau, Marc; Brasse, David
2015-11-15
Purpose: A new approach to proton computed tomography (pCT) is presented. In this approach, protons are not tracked one-by-one but a beam of particles is considered instead. The elements of the pCT reconstruction problem (residual energy and path) are redefined on the basis of this new approach. An analytical image reconstruction algorithm applicable to this scenario is also proposed. Methods: The pencil beam (PB) and its propagation in matter were modeled by making use of the generalization of the Fermi–Eyges theory to account for multiple Coulomb scattering (MCS). This model was integrated into the pCT reconstruction problem, allowing the definition of the mean beam path concept similar to the most likely path (MLP) used in the single-particle approach. A numerical validation of the model was performed. The algorithm of filtered backprojection along MLPs was adapted to the beam-by-beam approach. The acquisition of a perfect proton scan was simulated and the data were used to reconstruct images of the relative stopping power of the phantom with the single-proton and beam-by-beam approaches. The resulting images were compared in a qualitative way. Results: The parameters of the modeled PB (mean and spread) were compared to Monte Carlo results in order to validate the model. For a water target, good agreement was found for the mean value of the distributions. As far as the spread is concerned, depth-dependent discrepancies as large as 2%–3% were found. For a heterogeneous phantom, discrepancies in the distribution spread ranged from 6% to 8%. The image reconstructed with the beam-by-beam approach showed a high level of noise compared to the one reconstructed with the classical approach. Conclusions: The PB approach to proton imaging may allow technical challenges imposed by the current proton-by-proton method to be overcome. In this framework, an analytical algorithm is proposed. Further work will involve a detailed study of the performances and limitations of
The process group approach to reliable distributed computing
NASA Technical Reports Server (NTRS)
Birman, Kenneth P.
1991-01-01
The difficulty of developing reliable distributed software is an impediment to applying distributed computing technology in many settings. Experience with the ISIS system suggests that a structured approach based on virtually synchronous process groups yields systems which are substantially easier to develop, fault-tolerance, and self-managing. Six years of research on ISIS are reviewed, describing the model, the types of applications to which ISIS was applied, and some of the reasoning that underlies a recent effort to redesign and reimplement ISIS as a much smaller, lightweight system.
Computational systems biology approaches to anti-angiogenic cancer therapeutics.
Finley, Stacey D; Chu, Liang-Hui; Popel, Aleksander S
2015-02-01
Angiogenesis is an exquisitely regulated process that is required for physiological processes and is also important in numerous diseases. Tumors utilize angiogenesis to generate the vascular network needed to supply the cancer cells with nutrients and oxygen, and many cancer drugs aim to inhibit tumor angiogenesis. Anti-angiogenic therapy involves inhibiting multiple cell types, molecular targets, and intracellular signaling pathways. Computational tools are useful in guiding treatment strategies, predicting the response to treatment, and identifying new targets of interest. Here, we describe progress that has been made in applying mathematical modeling and bioinformatics approaches to study anti-angiogenic therapeutics in cancer.
Identification of Protein–Excipient Interaction Hotspots Using Computational Approaches
Barata, Teresa S.; Zhang, Cheng; Dalby, Paul A.; Brocchini, Steve; Zloh, Mire
2016-01-01
Protein formulation development relies on the selection of excipients that inhibit protein–protein interactions preventing aggregation. Empirical strategies involve screening many excipient and buffer combinations using force degradation studies. Such methods do not readily provide information on intermolecular interactions responsible for the protective effects of excipients. This study describes a molecular docking approach to screen and rank interactions allowing for the identification of protein–excipient hotspots to aid in the selection of excipients to be experimentally screened. Previously published work with Drosophila Su(dx) was used to develop and validate the computational methodology, which was then used to determine the formulation hotspots for Fab A33. Commonly used excipients were examined and compared to the regions in Fab A33 prone to protein–protein interactions that could lead to aggregation. This approach could provide information on a molecular level about the protective interactions of excipients in protein formulations to aid the more rational development of future formulations. PMID:27258262
Whole-genome CNV analysis: advances in computational approaches
Pirooznia, Mehdi; Goes, Fernando S.; Zandi, Peter P.
2015-01-01
Accumulating evidence indicates that DNA copy number variation (CNV) is likely to make a significant contribution to human diversity and also play an important role in disease susceptibility. Recent advances in genome sequencing technologies have enabled the characterization of a variety of genomic features, including CNVs. This has led to the development of several bioinformatics approaches to detect CNVs from next-generation sequencing data. Here, we review recent advances in CNV detection from whole genome sequencing. We discuss the informatics approaches and current computational tools that have been developed as well as their strengths and limitations. This review will assist researchers and analysts in choosing the most suitable tools for CNV analysis as well as provide suggestions for new directions in future development. PMID:25918519
Computational approaches to understand cardiac electrophysiology and arrhythmias
Roberts, Byron N.; Yang, Pei-Chi; Behrens, Steven B.; Moreno, Jonathan D.
2012-01-01
Cardiac rhythms arise from electrical activity generated by precisely timed opening and closing of ion channels in individual cardiac myocytes. These impulses spread throughout the cardiac muscle to manifest as electrical waves in the whole heart. Regularity of electrical waves is critically important since they signal the heart muscle to contract, driving the primary function of the heart to act as a pump and deliver blood to the brain and vital organs. When electrical activity goes awry during a cardiac arrhythmia, the pump does not function, the brain does not receive oxygenated blood, and death ensues. For more than 50 years, mathematically based models of cardiac electrical activity have been used to improve understanding of basic mechanisms of normal and abnormal cardiac electrical function. Computer-based modeling approaches to understand cardiac activity are uniquely helpful because they allow for distillation of complex emergent behaviors into the key contributing components underlying them. Here we review the latest advances and novel concepts in the field as they relate to understanding the complex interplay between electrical, mechanical, structural, and genetic mechanisms during arrhythmia development at the level of ion channels, cells, and tissues. We also discuss the latest computational approaches to guiding arrhythmia therapy. PMID:22886409
Crowd Computing as a Cooperation Problem: An Evolutionary Approach
NASA Astrophysics Data System (ADS)
Christoforou, Evgenia; Fernández Anta, Antonio; Georgiou, Chryssis; Mosteiro, Miguel A.; Sánchez, Angel
2013-05-01
Cooperation is one of the socio-economic issues that has received more attention from the physics community. The problem has been mostly considered by studying games such as the Prisoner's Dilemma or the Public Goods Game. Here, we take a step forward by studying cooperation in the context of crowd computing. We introduce a model loosely based on Principal-agent theory in which people (workers) contribute to the solution of a distributed problem by computing answers and reporting to the problem proposer (master). To go beyond classical approaches involving the concept of Nash equilibrium, we work on an evolutionary framework in which both the master and the workers update their behavior through reinforcement learning. Using a Markov chain approach, we show theoretically that under certain----not very restrictive—conditions, the master can ensure the reliability of the answer resulting of the process. Then, we study the model by numerical simulations, finding that convergence, meaning that the system reaches a point in which it always produces reliable answers, may in general be much faster than the upper bounds given by the theoretical calculation. We also discuss the effects of the master's level of tolerance to defectors, about which the theory does not provide information. The discussion shows that the system works even with very large tolerances. We conclude with a discussion of our results and possible directions to carry this research further.
Tensor scale: An analytic approach with efficient computation and applications☆
Xu, Ziyue; Saha, Punam K.; Dasgupta, Soura
2015-01-01
Scale is a widely used notion in computer vision and image understanding that evolved in the form of scale-space theory where the key idea is to represent and analyze an image at various resolutions. Recently, we introduced a notion of local morphometric scale referred to as “tensor scale” using an ellipsoidal model that yields a unified representation of structure size, orientation and anisotropy. In the previous work, tensor scale was described using a 2-D algorithmic approach and a precise analytic definition was missing. Also, the application of tensor scale in 3-D using the previous framework is not practical due to high computational complexity. In this paper, an analytic definition of tensor scale is formulated for n-dimensional (n-D) images that captures local structure size, orientation and anisotropy. Also, an efficient computational solution in 2- and 3-D using several novel differential geometric approaches is presented and the accuracy of results is experimentally examined. Also, a matrix representation of tensor scale is derived facilitating several operations including tensor field smoothing to capture larger contextual knowledge. Finally, the applications of tensor scale in image filtering and n-linear interpolation are presented and the performance of their results is examined in comparison with respective state-of-art methods. Specifically, the performance of tensor scale based image filtering is compared with gradient and Weickert’s structure tensor based diffusive filtering algorithms. Also, the performance of tensor scale based n-linear interpolation is evaluated in comparison with standard n-linear and windowed-sinc interpolation methods. PMID:26236148
Computing Optimal Stochastic Portfolio Execution Strategies: A Parametric Approach Using Simulations
NASA Astrophysics Data System (ADS)
Moazeni, Somayeh; Coleman, Thomas F.; Li, Yuying
2010-09-01
Computing optimal stochastic portfolio execution strategies under appropriate risk consideration presents great computational challenge. We investigate a parametric approach for computing optimal stochastic strategies using Monte Carlo simulations. This approach allows reduction in computational complexity by computing coefficients for a parametric representation of a stochastic dynamic strategy based on static optimization. Using this technique, constraints can be similarly handled using appropriate penalty functions. We illustrate the proposed approach to minimize the expected execution cost and Conditional Value-at-Risk (CVaR).
Automated Approach to Very High-Order Aeroacoustic Computations. Revision
NASA Technical Reports Server (NTRS)
Dyson, Rodger W.; Goodrich, John W.
2001-01-01
Computational aeroacoustics requires efficient, high-resolution simulation tools. For smooth problems, this is best accomplished with very high-order in space and time methods on small stencils. However, the complexity of highly accurate numerical methods can inhibit their practical application, especially in irregular geometries. This complexity is reduced by using a special form of Hermite divided-difference spatial interpolation on Cartesian grids, and a Cauchy-Kowalewski recursion procedure for time advancement. In addition, a stencil constraint tree reduces the complexity of interpolating grid points that am located near wall boundaries. These procedures are used to develop automatically and to implement very high-order methods (> 15) for solving the linearized Euler equations that can achieve less than one grid point per wavelength resolution away from boundaries by including spatial derivatives of the primitive variables at each grid point. The accuracy of stable surface treatments is currently limited to 11th order for grid aligned boundaries and to 2nd order for irregular boundaries.
a Holistic Approach for Inspection of Civil Infrastructures Based on Computer Vision Techniques
NASA Astrophysics Data System (ADS)
Stentoumis, C.; Protopapadakis, E.; Doulamis, A.; Doulamis, N.
2016-06-01
In this work, it is examined the 2D recognition and 3D modelling of concrete tunnel cracks, through visual cues. At the time being, the structural integrity inspection of large-scale infrastructures is mainly performed through visual observations by human inspectors, who identify structural defects, rate them and, then, categorize their severity. The described approach targets at minimum human intervention, for autonomous inspection of civil infrastructures. The shortfalls of existing approaches in crack assessment are being addressed by proposing a novel detection scheme. Although efforts have been made in the field, synergies among proposed techniques are still missing. The holistic approach of this paper exploits the state of the art techniques of pattern recognition and stereo-matching, in order to build accurate 3D crack models. The innovation lies in the hybrid approach for the CNN detector initialization, and the use of the modified census transformation for stereo matching along with a binary fusion of two state-of-the-art optimization schemes. The described approach manages to deal with images of harsh radiometry, along with severe radiometric differences in the stereo pair. The effectiveness of this workflow is evaluated on a real dataset gathered in highway and railway tunnels. What is promising is that the computer vision workflow described in this work can be transferred, with adaptations of course, to other infrastructure such as pipelines, bridges and large industrial facilities that are in the need of continuous state assessment during their operational life cycle.
Computational approaches for microalgal biofuel optimization: a review.
Koussa, Joseph; Chaiboonchoe, Amphun; Salehi-Ashtiani, Kourosh
2014-01-01
The increased demand and consumption of fossil fuels have raised interest in finding renewable energy sources throughout the globe. Much focus has been placed on optimizing microorganisms and primarily microalgae, to efficiently produce compounds that can substitute for fossil fuels. However, the path to achieving economic feasibility is likely to require strain optimization through using available tools and technologies in the fields of systems and synthetic biology. Such approaches invoke a deep understanding of the metabolic networks of the organisms and their genomic and proteomic profiles. The advent of next generation sequencing and other high throughput methods has led to a major increase in availability of biological data. Integration of such disparate data can help define the emergent metabolic system properties, which is of crucial importance in addressing biofuel production optimization. Herein, we review major computational tools and approaches developed and used in order to potentially identify target genes, pathways, and reactions of particular interest to biofuel production in algae. As the use of these tools and approaches has not been fully implemented in algal biofuel research, the aim of this review is to highlight the potential utility of these resources toward their future implementation in algal research.
Computational approaches for microalgal biofuel optimization: a review.
Koussa, Joseph; Chaiboonchoe, Amphun; Salehi-Ashtiani, Kourosh
2014-01-01
The increased demand and consumption of fossil fuels have raised interest in finding renewable energy sources throughout the globe. Much focus has been placed on optimizing microorganisms and primarily microalgae, to efficiently produce compounds that can substitute for fossil fuels. However, the path to achieving economic feasibility is likely to require strain optimization through using available tools and technologies in the fields of systems and synthetic biology. Such approaches invoke a deep understanding of the metabolic networks of the organisms and their genomic and proteomic profiles. The advent of next generation sequencing and other high throughput methods has led to a major increase in availability of biological data. Integration of such disparate data can help define the emergent metabolic system properties, which is of crucial importance in addressing biofuel production optimization. Herein, we review major computational tools and approaches developed and used in order to potentially identify target genes, pathways, and reactions of particular interest to biofuel production in algae. As the use of these tools and approaches has not been fully implemented in algal biofuel research, the aim of this review is to highlight the potential utility of these resources toward their future implementation in algal research. PMID:25309916
Suggested Approaches to the Measurement of Computer Anxiety.
ERIC Educational Resources Information Center
Toris, Carol
Psychologists can gain insight into human behavior by examining what people feel about, know about, and do with, computers. Two extreme reactions to computers are computer phobia, or anxiety, and computer addiction, or "hacking". A four-part questionnaire was developed to measure computer anxiety. The first part is a projective technique which…
Computer Modeling of Violent Intent: A Content Analysis Approach
Sanfilippo, Antonio P.; Mcgrath, Liam R.; Bell, Eric B.
2014-01-03
We present a computational approach to modeling the intent of a communication source representing a group or an individual to engage in violent behavior. Our aim is to identify and rank aspects of radical rhetoric that are endogenously related to violent intent to predict the potential for violence as encoded in written or spoken language. We use correlations between contentious rhetoric and the propensity for violent behavior found in documents from radical terrorist and non-terrorist groups and individuals to train and evaluate models of violent intent. We then apply these models to unseen instances of linguistic behavior to detect signs of contention that have a positive correlation with violent intent factors. Of particular interest is the application of violent intent models to social media, such as Twitter, that have proved to serve as effective channels in furthering sociopolitical change.
A general computational approach for repeat protein design.
Parmeggiani, Fabio; Huang, Po-Ssu; Vorobiev, Sergey; Xiao, Rong; Park, Keunwan; Caprari, Silvia; Su, Min; Seetharaman, Jayaraman; Mao, Lei; Janjua, Haleema; Montelione, Gaetano T; Hunt, John; Baker, David
2015-01-30
Repeat proteins have considerable potential for use as modular binding reagents or biomaterials in biomedical and nanotechnology applications. Here we describe a general computational method for building idealized repeats that integrates available family sequences and structural information with Rosetta de novo protein design calculations. Idealized designs from six different repeat families were generated and experimentally characterized; 80% of the proteins were expressed and soluble and more than 40% were folded and monomeric with high thermal stability. Crystal structures determined for members of three families are within 1Å root-mean-square deviation to the design models. The method provides a general approach for fast and reliable generation of stable modular repeat protein scaffolds. PMID:25451037
A General Computational Approach for Repeat Protein Design
Parmeggiani, Fabio; Huang, Po-Ssu; Vorobiev, Sergey; Xiao, Rong; Park, Keunwan; Caprari, Silvia; Su, Min; Jayaraman, Seetharaman; Mao, Lei; Janjua, Haleema; Montelione, Gaetano T.; Hunt, John; Baker, David
2014-01-01
Repeat proteins have considerable potential for use as modular binding reagents or biomaterials in biomedical and nanotechnology applications. Here we describe a general computational method for building idealized repeats that integrates available family sequences and structural information with Rosetta de novo protein design calculations. Idealized designs from six different repeat families were generated and experimentally characterized; 80% of the proteins were expressed and soluble and more than 40% were folded and monomeric with high thermal stability. Crystal structures determined for members of three families are within 1 Å root-mean-square deviation to the design models. The method provides a general approach for fast and reliable generation of stable modular repeat protein scaffolds. PMID:25451037
Systems approaches to computational modeling of the oral microbiome
Dimitrov, Dimiter V.
2013-01-01
Current microbiome research has generated tremendous amounts of data providing snapshots of molecular activity in a variety of organisms, environments, and cell types. However, turning this knowledge into whole system level of understanding on pathways and processes has proven to be a challenging task. In this review we highlight the applicability of bioinformatics and visualization techniques to large collections of data in order to better understand the information that contains related diet—oral microbiome—host mucosal transcriptome interactions. In particular, we focus on systems biology of Porphyromonas gingivalis in the context of high throughput computational methods tightly integrated with translational systems medicine. Those approaches have applications for both basic research, where we can direct specific laboratory experiments in model organisms and cell cultures, and human disease, where we can validate new mechanisms and biomarkers for prevention and treatment of chronic disorders. PMID:23847548
Computational approaches to study the effects of small genomic variations.
Khafizov, Kamil; Ivanov, Maxim V; Glazova, Olga V; Kovalenko, Sergei P
2015-10-01
Advances in DNA sequencing technologies have led to an avalanche-like increase in the number of gene sequences deposited in public databases over the last decade as well as the detection of an enormous number of previously unseen nucleotide variants therein. Given the size and complex nature of the genome-wide sequence variation data, as well as the rate of data generation, experimental characterization of the disease association of each of these variations or their effects on protein structure/function would be costly, laborious, time-consuming, and essentially impossible. Thus, in silico methods to predict the functional effects of sequence variations are constantly being developed. In this review, we summarize the major computational approaches and tools that are aimed at the prediction of the functional effect of mutations, and describe the state-of-the-art databases that can be used to obtain information about mutation significance. We also discuss future directions in this highly competitive field.
Computational Diagnostic: A Novel Approach to View Medical Data.
Mane, K. K.; Börner, K.
2007-01-01
A transition from traditional paper-based medical records to electronic health record is largely underway. The use of electronic records offers tremendous potential to personalize patient diagnosis and treatment. In this paper, we discuss a computational diagnostic tool that uses digital medical records to help doctors gain better insight about a patient's medical condition. The paper details different interactive features of the tool which offer potential to practice evidence-based medicine and advance patient diagnosis practices. The healthcare industry is a constantly evolving domain. Research from this domain is often translated into better understanding of different medical conditions. This new knowledge often contributes towards improved diagnosis and treatment solutions for patients. But the healthcare industry lags behind to seek immediate benefits of the new knowledge as it still adheres to the traditional paper-based approach to keep track of medical records. However recently we notice a drive that promotes a transition towards electronic health record (EHR). An EHR stores patient medical records in digital format and offers potential to replace the paper health records. Earlier attempts of an EHR replicated the paper layout on the screen, representation of medical history of a patient in a graphical time-series format, interactive visualization with 2D/3D generated images from an imaging device. But an EHR can be much more than just an 'electronic view' of the paper record or a collection of images from an imaging device. In this paper, we present an EHR called 'Computational Diagnostic Tool', that provides a novel computational approach to look at patient medical data. The developed EHR system is knowledge driven and acts as clinical decision support tool. The EHR tool provides two visual views of the medical data. Dynamic interaction with data is supported to help doctors practice evidence-based decisions and make judicious choices about patient
Molecular interactions and crystal packing in nematogen: Computational thermodynamic approach
NASA Astrophysics Data System (ADS)
Lakshmi Praveen, P.; Ojha, Durga P.
2011-10-01
A computational thermodynamic approach of molecular interactions in a nematogen p-n-alkyl benzoic acid ( nBAC) molecule with an alkyl group butyl (4BAC) has been carried out with respect to translational and orientational motion. The atomic net charge and dipole moment at each atomic center were evaluated using the complete neglect differential overlap (CNDO/2) method. The modified Rayleigh-Schrödinger perturbation theory along with multicentered-multipole expansion method were employed to evaluate long-range intermolecular interactions, while a 6-exp potential function was assumed for short-range interactions. Various possible geometrical arrangements of molecular pairs with regard to different energy components were considered, and the energetically favorable configuration was found to understand the crystal packing picture. Furthermore, these interaction energy values are taken as input to calculate the configurational entropy at room temperature (300 K), nematic-isotropic transition temperature (386 K) and above transition temperature (450 K) during different modes of interactions. An attempt has been made to describe interactions in a nematogen at molecular level, through which one can simplify the system to make the model computationally feasible in understanding the delicate interplay between energy and entropy, that accounts for mesomorphism and there by to analyze the molecular structure of a nematogen.
Itu, Lucian; Rapaka, Saikiran; Passerini, Tiziano; Georgescu, Bogdan; Schwemmer, Chris; Schoebinger, Max; Flohr, Thomas; Sharma, Puneet; Comaniciu, Dorin
2016-07-01
Fractional flow reserve (FFR) is a functional index quantifying the severity of coronary artery lesions and is clinically obtained using an invasive, catheter-based measurement. Recently, physics-based models have shown great promise in being able to noninvasively estimate FFR from patient-specific anatomical information, e.g., obtained from computed tomography scans of the heart and the coronary arteries. However, these models have high computational demand, limiting their clinical adoption. In this paper, we present a machine-learning-based model for predicting FFR as an alternative to physics-based approaches. The model is trained on a large database of synthetically generated coronary anatomies, where the target values are computed using the physics-based model. The trained model predicts FFR at each point along the centerline of the coronary tree, and its performance was assessed by comparing the predictions against physics-based computations and against invasively measured FFR for 87 patients and 125 lesions in total. Correlation between machine-learning and physics-based predictions was excellent (0.9994, P < 0.001), and no systematic bias was found in Bland-Altman analysis: mean difference was -0.00081 ± 0.0039. Invasive FFR ≤ 0.80 was found in 38 lesions out of 125 and was predicted by the machine-learning algorithm with a sensitivity of 81.6%, a specificity of 83.9%, and an accuracy of 83.2%. The correlation was 0.729 (P < 0.001). Compared with the physics-based computation, average execution time was reduced by more than 80 times, leading to near real-time assessment of FFR. Average execution time went down from 196.3 ± 78.5 s for the CFD model to ∼2.4 ± 0.44 s for the machine-learning model on a workstation with 3.4-GHz Intel i7 8-core processor.
Cloud computing approaches for prediction of ligand binding poses and pathways.
Lawrenz, Morgan; Shukla, Diwakar; Pande, Vijay S
2015-01-22
We describe an innovative protocol for ab initio prediction of ligand crystallographic binding poses and highly effective analysis of large datasets generated for protein-ligand dynamics. We include a procedure for setup and performance of distributed molecular dynamics simulations on cloud computing architectures, a model for efficient analysis of simulation data, and a metric for evaluation of model convergence. We give accurate binding pose predictions for five ligands ranging in affinity from 7 nM to > 200 μM for the immunophilin protein FKBP12, for expedited results in cases where experimental structures are difficult to produce. Our approach goes beyond single, low energy ligand poses to give quantitative kinetic information that can inform protein engineering and ligand design.
Towards scalable quantum communication and computation: Novel approaches and realizations
NASA Astrophysics Data System (ADS)
Jiang, Liang
Quantum information science involves exploration of fundamental laws of quantum mechanics for information processing tasks. This thesis presents several new approaches towards scalable quantum information processing. First, we consider a hybrid approach to scalable quantum computation, based on an optically connected network of few-qubit quantum registers. Specifically, we develop a novel scheme for scalable quantum computation that is robust against various imperfections. To justify that nitrogen-vacancy (NV) color centers in diamond can be a promising realization of the few-qubit quantum register, we show how to isolate a few proximal nuclear spins from the rest of the environment and use them for the quantum register. We also demonstrate experimentally that the nuclear spin coherence is only weakly perturbed under optical illumination, which allows us to implement quantum logical operations that use the nuclear spins to assist the repetitive-readout of the electronic spin. Using this technique, we demonstrate more than two-fold improvement in signal-to-noise ratio. Apart from direct application to enhance the sensitivity of the NV-based nano-magnetometer, this experiment represents an important step towards the realization of robust quantum information processors using electronic and nuclear spin qubits. We then study realizations of quantum repeaters for long distance quantum communication. Specifically, we develop an efficient scheme for quantum repeaters based on atomic ensembles. We use dynamic programming to optimize various quantum repeater protocols. In addition, we propose a new protocol of quantum repeater with encoding, which efficiently uses local resources (about 100 qubits) to identify and correct errors, to achieve fast one-way quantum communication over long distances. Finally, we explore quantum systems with topological order. Such systems can exhibit remarkable phenomena such as quasiparticles with anyonic statistics and have been proposed as
Computational approaches to protein inference in shotgun proteomics.
Li, Yong Fuga; Radivojac, Predrag
2012-01-01
Shotgun proteomics has recently emerged as a powerful approach to characterizing proteomes in biological samples. Its overall objective is to identify the form and quantity of each protein in a high-throughput manner by coupling liquid chromatography with tandem mass spectrometry. As a consequence of its high throughput nature, shotgun proteomics faces challenges with respect to the analysis and interpretation of experimental data. Among such challenges, the identification of proteins present in a sample has been recognized as an important computational task. This task generally consists of (1) assigning experimental tandem mass spectra to peptides derived from a protein database, and (2) mapping assigned peptides to proteins and quantifying the confidence of identified proteins. Protein identification is fundamentally a statistical inference problem with a number of methods proposed to address its challenges. In this review we categorize current approaches into rule-based, combinatorial optimization and probabilistic inference techniques, and present them using integer programming and Bayesian inference frameworks. We also discuss the main challenges of protein identification and propose potential solutions with the goal of spurring innovative research in this area. PMID:23176300
A computational approach for prediction of donor splice sites with improved accuracy.
Meher, Prabina Kumar; Sahu, Tanmaya Kumar; Rao, A R; Wahi, S D
2016-09-01
Identification of splice sites is important due to their key role in predicting the exon-intron structure of protein coding genes. Though several approaches have been developed for the prediction of splice sites, further improvement in the prediction accuracy will help predict gene structure more accurately. This paper presents a computational approach for prediction of donor splice sites with higher accuracy. In this approach, true and false splice sites were first encoded into numeric vectors and then used as input in artificial neural network (ANN), support vector machine (SVM) and random forest (RF) for prediction. ANN and SVM were found to perform equally and better than RF, while tested on HS3D and NN269 datasets. Further, the performance of ANN, SVM and RF were analyzed by using an independent test set of 50 genes and found that the prediction accuracy of ANN was higher than that of SVM and RF. All the predictors achieved higher accuracy while compared with the existing methods like NNsplice, MEM, MDD, WMM, MM1, FSPLICE, GeneID and ASSP, using the independent test set. We have also developed an online prediction server (PreDOSS) available at http://cabgrid.res.in:8080/predoss, for prediction of donor splice sites using the proposed approach. PMID:27302911
Computational approach in estimating the need of ditch network maintenance
NASA Astrophysics Data System (ADS)
Lauren, Ari; Hökkä, Hannu; Launiainen, Samuli; Palviainen, Marjo; Repo, Tapani; Leena, Finer; Piirainen, Sirpa
2015-04-01
Ditch network maintenance (DNM), implemented annually in 70 000 ha area in Finland, is the most controversial of all forest management practices. Nationwide, it is estimated to increase the forest growth by 1…3 million m3 per year, but simultaneously to cause 65 000 tons export of suspended solids and 71 tons of phosphorus (P) to water courses. A systematic approach that allows simultaneous quantification of the positive and negative effects of DNM is required. Excess water in the rooting zone slows the gas exchange and decreases biological activity interfering with the forest growth in boreal forested peatlands. DNM is needed when: 1) the excess water in the rooting zone restricts the forest growth before the DNM, and 2) after the DNM the growth restriction ceases or decreases, and 3) the benefits of DNM are greater than the caused adverse effects. Aeration in the rooting zone can be used as a drainage criterion. Aeration is affected by several factors such as meteorological conditions, tree stand properties, hydraulic properties of peat, ditch depth, and ditch spacing. We developed a 2-dimensional DNM simulator that allows the user to adjust these factors and to evaluate their effect on the soil aeration at different distance from the drainage ditch. DNM simulator computes hydrological processes and soil aeration along a water flowpath between two ditches. Applying daily time step it calculates evapotranspiration, snow accumulation and melt, infiltration, soil water storage, ground water level, soil water content, air-filled porosity and runoff. The model performance in hydrology has been tested against independent high frequency field monitoring data. Soil aeration at different distance from the ditch is computed under steady-state assumption using an empirical oxygen consumption model, simulated air-filled porosity, and diffusion coefficient at different depths in soil. Aeration is adequate and forest growth rate is not limited by poor aeration if the
An Evolutionary Computation Approach to Examine Functional Brain Plasticity
Roy, Arnab; Campbell, Colin; Bernier, Rachel A.; Hillary, Frank G.
2016-01-01
One common research goal in systems neurosciences is to understand how the functional relationship between a pair of regions of interest (ROIs) evolves over time. Examining neural connectivity in this way is well-suited for the study of developmental processes, learning, and even in recovery or treatment designs in response to injury. For most fMRI based studies, the strength of the functional relationship between two ROIs is defined as the correlation between the average signal representing each region. The drawback to this approach is that much information is lost due to averaging heterogeneous voxels, and therefore, the functional relationship between a ROI-pair that evolve at a spatial scale much finer than the ROIs remain undetected. To address this shortcoming, we introduce a novel evolutionary computation (EC) based voxel-level procedure to examine functional plasticity between an investigator defined ROI-pair by simultaneously using subject-specific BOLD-fMRI data collected from two sessions seperated by finite duration of time. This data-driven procedure detects a sub-region composed of spatially connected voxels from each ROI (a so-called sub-regional-pair) such that the pair shows a significant gain/loss of functional relationship strength across the two time points. The procedure is recursive and iteratively finds all statistically significant sub-regional-pairs within the ROIs. Using this approach, we examine functional plasticity between the default mode network (DMN) and the executive control network (ECN) during recovery from traumatic brain injury (TBI); the study includes 14 TBI and 12 healthy control subjects. We demonstrate that the EC based procedure is able to detect functional plasticity where a traditional averaging based approach fails. The subject-specific plasticity estimates obtained using the EC-procedure are highly consistent across multiple runs. Group-level analyses using these plasticity estimates showed an increase in the strength
An Evolutionary Computation Approach to Examine Functional Brain Plasticity.
Roy, Arnab; Campbell, Colin; Bernier, Rachel A; Hillary, Frank G
2016-01-01
One common research goal in systems neurosciences is to understand how the functional relationship between a pair of regions of interest (ROIs) evolves over time. Examining neural connectivity in this way is well-suited for the study of developmental processes, learning, and even in recovery or treatment designs in response to injury. For most fMRI based studies, the strength of the functional relationship between two ROIs is defined as the correlation between the average signal representing each region. The drawback to this approach is that much information is lost due to averaging heterogeneous voxels, and therefore, the functional relationship between a ROI-pair that evolve at a spatial scale much finer than the ROIs remain undetected. To address this shortcoming, we introduce a novel evolutionary computation (EC) based voxel-level procedure to examine functional plasticity between an investigator defined ROI-pair by simultaneously using subject-specific BOLD-fMRI data collected from two sessions seperated by finite duration of time. This data-driven procedure detects a sub-region composed of spatially connected voxels from each ROI (a so-called sub-regional-pair) such that the pair shows a significant gain/loss of functional relationship strength across the two time points. The procedure is recursive and iteratively finds all statistically significant sub-regional-pairs within the ROIs. Using this approach, we examine functional plasticity between the default mode network (DMN) and the executive control network (ECN) during recovery from traumatic brain injury (TBI); the study includes 14 TBI and 12 healthy control subjects. We demonstrate that the EC based procedure is able to detect functional plasticity where a traditional averaging based approach fails. The subject-specific plasticity estimates obtained using the EC-procedure are highly consistent across multiple runs. Group-level analyses using these plasticity estimates showed an increase in the strength
Brounstein, Anna; Hacihaliloglu, Ilker; Guy, Pierre; Hodgson, Antony; Abugharbieh, Rafeef
2015-12-01
Automatic, accurate and real-time registration is an important step in providing effective guidance and successful anatomic restoration in ultrasound (US)-based computer assisted orthopedic surgery. We propose a method in which local phase-based bone surfaces, extracted from intra-operative US data, are registered to pre-operatively segmented computed tomography data. Extracted bone surfaces are downsampled and reinforced with high curvature features. A novel hierarchical simplification algorithm is used to further optimize the point clouds. The final point clouds are represented as Gaussian mixture models and iteratively matched by minimizing the dissimilarity between them using an L2 metric. For 44 clinical data sets from 25 pelvic fracture patients and 49 phantom data sets, we report mean surface registration accuracies of 0.31 and 0.77 mm, respectively, with an average registration time of 1.41 s. Our results suggest the viability and potential of the chosen method for real-time intra-operative registration in orthopedic surgery.
Brounstein, Anna; Hacihaliloglu, Ilker; Guy, Pierre; Hodgson, Antony; Abugharbieh, Rafeef
2015-12-01
Automatic, accurate and real-time registration is an important step in providing effective guidance and successful anatomic restoration in ultrasound (US)-based computer assisted orthopedic surgery. We propose a method in which local phase-based bone surfaces, extracted from intra-operative US data, are registered to pre-operatively segmented computed tomography data. Extracted bone surfaces are downsampled and reinforced with high curvature features. A novel hierarchical simplification algorithm is used to further optimize the point clouds. The final point clouds are represented as Gaussian mixture models and iteratively matched by minimizing the dissimilarity between them using an L2 metric. For 44 clinical data sets from 25 pelvic fracture patients and 49 phantom data sets, we report mean surface registration accuracies of 0.31 and 0.77 mm, respectively, with an average registration time of 1.41 s. Our results suggest the viability and potential of the chosen method for real-time intra-operative registration in orthopedic surgery. PMID:26365924
Zhang, Xinyue; Lourenco, Daniela; Aguilar, Ignacio; Legarra, Andres; Misztal, Ignacy
2016-01-01
former. Manhattan plots had higher resolution with 5 and 100 QTL. Using a common weight for a window of 20 SNP that sums or averages the SNP variance enhances accuracy of predicting GEBV and provides accurate estimation of marker effects. PMID:27594861
Zhang, Xinyue; Lourenco, Daniela; Aguilar, Ignacio; Legarra, Andres; Misztal, Ignacy
2016-01-01
. Manhattan plots had higher resolution with 5 and 100 QTL. Using a common weight for a window of 20 SNP that sums or averages the SNP variance enhances accuracy of predicting GEBV and provides accurate estimation of marker effects.
Zhang, Xinyue; Lourenco, Daniela; Aguilar, Ignacio; Legarra, Andres; Misztal, Ignacy
2016-01-01
. Manhattan plots had higher resolution with 5 and 100 QTL. Using a common weight for a window of 20 SNP that sums or averages the SNP variance enhances accuracy of predicting GEBV and provides accurate estimation of marker effects. PMID:27594861
Zhang, Xinyue; Lourenco, Daniela; Aguilar, Ignacio; Legarra, Andres; Misztal, Ignacy
2016-01-01
former. Manhattan plots had higher resolution with 5 and 100 QTL. Using a common weight for a window of 20 SNP that sums or averages the SNP variance enhances accuracy of predicting GEBV and provides accurate estimation of marker effects.
NASA Astrophysics Data System (ADS)
Leal, Allan M. M.; Kulik, Dmitrii A.; Kosakowski, Georg
2016-02-01
We present a numerical method for multiphase chemical equilibrium calculations based on a Gibbs energy minimization approach. The method can accurately and efficiently determine the stable phase assemblage at equilibrium independently of the type of phases and species that constitute the chemical system. We have successfully applied our chemical equilibrium algorithm in reactive transport simulations to demonstrate its effective use in computationally intensive applications. We used FEniCS to solve the governing partial differential equations of mass transport in porous media using finite element methods in unstructured meshes. Our equilibrium calculations were benchmarked with GEMS3K, the numerical kernel of the geochemical package GEMS. This allowed us to compare our results with a well-established Gibbs energy minimization algorithm, as well as their performance on every mesh node, at every time step of the transport simulation. The benchmark shows that our novel chemical equilibrium algorithm is accurate, robust, and efficient for reactive transport applications, and it is an improvement over the Gibbs energy minimization algorithm used in GEMS3K. The proposed chemical equilibrium method has been implemented in Reaktoro, a unified framework for modeling chemically reactive systems, which is now used as an alternative numerical kernel of GEMS.
Villa-Camacho, Juan C; Iyoha-Bello, Otatade; Behrouzi, Shohreh; Snyder, Brian D; Nazarian, Ara
2014-01-01
The assessment of fracture risk in patients afflicted with osseous neoplasms has long presented a problem for orthopedic oncologists. These patients are at risk for developing pathologic fractures through lytic defects in the appendicular and axial skeleton with devastating consequences on their quality of life. Lesions with a high risk of fracture may require prophylactic surgical stabilization, whereas low-risk lesions can be treated conservatively. Therefore, effective prevention of pathologic fractures depends on accurate assessment of fracture risk and is a critical step to avoid debilitating complications. Given the complex nature of osseous neoplasms, treatment requires a multidisciplinary approach; yet, little consensus regarding fracture risk assessment exists among physicians involved in the care of these patients. In order to improve the overall standard of care, specific criteria must be adopted to formulate consistent and accurate fracture risk predictions. However, clinicians make subjective assessments about fracture risk on plain radiographs using guidelines now recognized to be inaccurate. Osseous neoplasms alter both the material and geometric properties of bone; failure to account for changes in both of these parameters limits the accuracy of current fracture risk assessments. Rigidity, the capacity to resist deformation upon loading, is a structural property that integrates both the material and geometric properties of bone. Therefore, rigidity can be used as a mechanical assay of the changes induced by lytic lesions to the structural competency of bone. Using this principle, computed tomography (CT)-based structural rigidity analysis (CTRA) was developed and validated in a series of preclinical and clinical studies. PMID:25396051
Xu, Hong-En; Zhang, Hua-Hao; Han, Min-Jin; Shen, Yi-Hong; Huang, Xian-Zhi; Xiang, Zhong-Huai; Zhang, Ze
2012-08-01
Repetitive sequences (repeats) represent a significant fraction of the eukaryotic genomes and can be divided into tandem repeats, segmental duplications, and interspersed repeats on the basis of their sequence characteristics and how they are formed. Most interspersed repeats are derived from transposable elements (TEs). Eukaryotic TEs have been subdivided into two major classes according to the intermediate they use to move. The transposition and amplification of TEs have a great impact on the evolution of genes and the stability of genomes. However, identification and classification of TEs are complex and difficult due to the fact that their structure and classification are complex and diverse compared with those of other types of repeats. Here, we briefly introduced the function and classification of TEs, and summarized three different steps for identification, classification and annotation of TEs in eukaryotic genomes: (1) assembly of a repeat library, (2) repeat correction and classification, and (3) genome annotation. The existing computational approaches for each step were summarized and the advantages and disadvantages of the approaches were also highlighted in this review. To accurately identify, classify, and annotate the TEs in eukaryotic genomes requires combined methods. This review provides useful information for biologists who are not familiar with these approaches to find their way through the forest of programs.
A computational approach to mechanistic and predictive toxicology of pesticides.
Kongsbak, Kristine; Vinggaard, Anne Marie; Hadrup, Niels; Audouze, Karine
2014-01-01
Emerging challenges of managing and interpreting large amounts of complex biological data have given rise to the growing field of computational biology. We investigated the applicability of an integrated systems toxicology approach on five selected pesticides to get an overview of their modes of action in humans, to group them according to their modes of action, and to hypothesize on their potential effects on human health. We extracted human proteins associated to prochloraz, tebuconazole, epoxiconazole, procymidone, and mancozeb and enriched each protein set by using a high confidence human protein interactome. Then, we explored modes of action of the chemicals, by integrating protein-disease information to the resulting protein networks. The dominating human adverse effects affected were reproductive disorders followed by adrenal diseases. Our results indicated that prochloraz, tebuconazole, and procymidone exerted their effects mainly via interference with steroidogenesis and nuclear receptors. Prochloraz was associated to a large number of human diseases, and together with tebuconazole showed several significant associations to Testicular Dysgenesis Syndrome. Mancozeb showed a differential mode of action, involving inflammatory processes. This method provides an efficient way of overviewing data and grouping chemicals according to their mode of action and potential human adverse effects. Such information is valuable when dealing with predictions of mixture effects of chemicals and may contribute to the development of adverse outcome pathways. PMID:24037280
Applying a cloud computing approach to storage architectures for spacecraft
NASA Astrophysics Data System (ADS)
Baldor, Sue A.; Quiroz, Carlos; Wood, Paul
As sensor technologies, processor speeds, and memory densities increase, spacecraft command, control, processing, and data storage systems have grown in complexity to take advantage of these improvements and expand the possible missions of spacecraft. Spacecraft systems engineers are increasingly looking for novel ways to address this growth in complexity and mitigate associated risks. Looking to conventional computing, many solutions have been executed to solve both the problem of complexity and heterogeneity in systems. In particular, the cloud-based paradigm provides a solution for distributing applications and storage capabilities across multiple platforms. In this paper, we propose utilizing a cloud-like architecture to provide a scalable mechanism for providing mass storage in spacecraft networks that can be reused on multiple spacecraft systems. By presenting a consistent interface to applications and devices that request data to be stored, complex systems designed by multiple organizations may be more readily integrated. Behind the abstraction, the cloud storage capability would manage wear-leveling, power consumption, and other attributes related to the physical memory devices, critical components in any mass storage solution for spacecraft. Our approach employs SpaceWire networks and SpaceWire-capable devices, although the concept could easily be extended to non-heterogeneous networks consisting of multiple spacecraft and potentially the ground segment.
A systems approach to computer-based training
NASA Technical Reports Server (NTRS)
Drape, Gaylen W.
1994-01-01
This paper describes the hardware and software systems approach used in the Automated Recertification Training System (ARTS), a Phase 2 Small Business Innovation Research (SBIR) project for NASA Kennedy Space Center (KSC). The goal of this project is to optimize recertification training of technicians who process the Space Shuttle before launch by providing computer-based training courseware. The objectives of ARTS are to implement more effective CBT applications identified through a need assessment process and to provide an ehanced courseware production system. The system's capabilities are demonstrated by using five different pilot applications to convert existing classroom courses into interactive courseware. When the system is fully implemented at NASA/KSC, trainee job performance will improve and the cost of courseware development will be lower. Commercialization of the technology developed as part of this SBIR project is planned for Phase 3. Anticipated spin-off products include custom courseware for technical skills training and courseware production software for use by corporate training organizations of aerospace and other industrial companies.
A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors
Gayvert, Kaitlyn; Dardenne, Etienne; Cheung, Cynthia; Boland, Mary Regina; Lorberbaum, Tal; Wanjala, Jackline; Chen, Yu; Rubin, Mark; Tatonetti, Nicholas P.; Rickman, David; Elemento, Olivier
2016-01-01
Summary Mutations in transcription factors (TFs) genes are frequently observed in tumors, often leading to aberrant transcriptional activity. Unfortunately, TFs are often considered undruggable due to the absence of targetable enzymatic activity. To address this problem, we developed CRAFTT, a Computational drug-Repositioning Approach For Targeting Transcription factor activity. CRAFTT combines ChIP-seq with drug-induced expression profiling to identify small molecules that can specifically perturb TF activity. Application to ENCODE ChIP-seq datasets revealed known drug-TF interactions and a global drug-protein network analysis further supported these predictions. Application of CRAFTT to ERG, a pro-invasive, frequently over-expressed oncogenic TF predicted that dexamethasone would inhibit ERG activity. Indeed, dexamethasone significantly decreased cell invasion and migration in an ERG-dependent manner. Furthermore, analysis of Electronic Medical Record data indicates a protective role for dexamethasone against prostate cancer. Altogether, our method provides a broadly applicable strategy to identify drugs that specifically modulate TF activity. PMID:27264179
Lexical is as lexical does: computational approaches to lexical representation
Woollams, Anna M.
2015-01-01
In much of neuroimaging and neuropsychology, regions of the brain have been associated with ‘lexical representation’, with little consideration as to what this cognitive construct actually denotes. Within current computational models of word recognition, there are a number of different approaches to the representation of lexical knowledge. Structural lexical representations, found in original theories of word recognition, have been instantiated in modern localist models. However, such a representational scheme lacks neural plausibility in terms of economy and flexibility. Connectionist models have therefore adopted distributed representations of form and meaning. Semantic representations in connectionist models necessarily encode lexical knowledge. Yet when equipped with recurrent connections, connectionist models can also develop attractors for familiar forms that function as lexical representations. Current behavioural, neuropsychological and neuroimaging evidence shows a clear role for semantic information, but also suggests some modality- and task-specific lexical representations. A variety of connectionist architectures could implement these distributed functional representations, and further experimental and simulation work is required to discriminate between these alternatives. Future conceptualisations of lexical representations will therefore emerge from a synergy between modelling and neuroscience. PMID:25893204
Computer vision approach to detect colonic polyps in computed tomographic colonography
NASA Astrophysics Data System (ADS)
McKenna, Matthew T.; Wang, Shijun; Nguyen, Tan B.; Burns, Joseph E.; Petrick, Nicholas; Sahiner, Berkman; Summers, Ronald M.
2012-03-01
In this paper, we present evaluation results for a novel colonic polyp classification method for use as part of a computed tomographic colonography (CTC) computer-aided detection (CAD) algorithm. Inspired by the interpretative methodology of radiologists using 3D fly-through mode in CTC reading, we have developed an algorithm which utilizes sequences of images (referred to here as videos) for classification of CAD marks. First, we generated an initial list of polyp candidates using an existing CAD system. For each of these candidates, we created a video composed of a series of intraluminal, volume-rendered images focusing on the candidate from multiple viewpoints. These videos illustrated the shape of the polyp candidate and gathered contextual information of diagnostic importance. We calculated the histogram of oriented gradients (HOG) feature on each frame of the video and utilized a support vector machine for classification. We tested our method by analyzing a CTC data set of 50 patients from three medical centers. Our proposed video analysis method for polyp classification showed significantly better performance than an approach using only the 2D CT slice data. The areas under the ROC curve for these methods were 0.88 (95% CI: [0.84, 0.91]) and 0.80 (95% CI: [0.75, 0.84]) respectively (p=0.0005).
The Computer in Library Education: One School's Approach.
ERIC Educational Resources Information Center
Drott, M. Carl
The increasing presence and use of computers in libraries has brought about the more frequent introduction of computers and their uses into library education. The Drexel University Graduate School of Library Science has introduced the computer into the curriculum more through individual experimentation and innovation than by planned development.…
An Educational Approach to Computationally Modeling Dynamical Systems
ERIC Educational Resources Information Center
Chodroff, Leah; O'Neal, Tim M.; Long, David A.; Hemkin, Sheryl
2009-01-01
Chemists have used computational science methodologies for a number of decades and their utility continues to be unabated. For this reason we developed an advanced lab in computational chemistry in which students gain understanding of general strengths and weaknesses of computation-based chemistry by working through a specific research problem.…
Computational approaches to stochastic systems in physics and biology
NASA Astrophysics Data System (ADS)
Jeraldo Maldonado, Patricio Rodrigo
In this dissertation, I devise computational approaches to model and understand two very different systems which exhibit stochastic behavior: quantum fluids with topological defects arising during quenches and forcing, and complex microbial communities living and evolving with the gastrointestinal tracts of vertebrates. As such, this dissertation is organized into two parts. In Part I, I create a model for quantum fluids, which incorporates a conservative and dissipative part, and I also allow the fluid to be externally forced by a normal fluid. I use then this model to calculate scaling laws arising from the stochastic interactions of the topological defects exhibited by the modeled fluid while undergoing a quench. In Chapter 2 I give a detailed description of this model of quantum fluids. Unlike more traditional approaches, this model is based on Cell Dynamical Systems (CDS), an approach that captures relevant physical features of the system and allows for long time steps during its evolution. I devise a two step CDS model, implementing both conservative and dissipative dynamics present in quantum fluids. I also couple the model with an external normal fluid field that drives the system. I then validate the results of the model by measuring different scaling laws predicted for quantum fluids. I also propose an extension of the model that also incorporates the excitations of the fluid and couples its dynamics with the dynamics of the condensate. In Chapter 3 I use the above model to calculate scaling laws predicted for the velocity of topological defects undergoing a critical quench. To accomplish this, I numerically implement an algorithm that extracts from the order parameter field the velocity components of the defects as they move during the quench process. This algorithm is robust and extensible to any system where defects are located by the zeros of the order parameter. The algorithm is also applied to a sheared stripe-forming system, allowing the
Novel Approaches in Astrocyte Protection: from Experimental Methods to Computational Approaches.
Garzón, Daniel; Cabezas, Ricardo; Vega, Nelson; Ávila-Rodriguez, Marcos; Gonzalez, Janneth; Gómez, Rosa Margarita; Echeverria, Valentina; Aliev, Gjumrakch; Barreto, George E
2016-04-01
Astrocytes are important for normal brain functioning. Astrocytes are metabolic regulators of the brain that exert many functions such as the preservation of blood-brain barrier (BBB) function, clearance of toxic substances, and generation of antioxidant molecules and growth factors. These functions are fundamental to sustain the function and survival of neurons and other brain cells. For these reasons, the protection of astrocytes has become relevant for the prevention of neuronal death during brain pathologies such as Parkinson's disease, Alzheimer's disease, stroke, and other neurodegenerative conditions. Currently, different strategies are being used to protect the main astrocytic functions during neurological diseases, including the use of growth factors, steroid derivatives, mesenchymal stem cell paracrine factors, nicotine derivatives, and computational biology tools. Moreover, the combined use of experimental approaches with bioinformatics tools such as the ones obtained through system biology has allowed a broader knowledge in astrocytic protection both in normal and pathological conditions. In the present review, we highlight some of these recent paradigms in assessing astrocyte protection using experimental and computational approaches and discuss how they could be used for the study of restorative therapies for the brain in pathological conditions.
NASA Astrophysics Data System (ADS)
Je, U. K.; Cho, H. M.; Cho, H. S.; Park, Y. O.; Park, C. K.; Lim, H. W.; Kim, K. S.; Kim, G. A.; Park, S. Y.; Woo, T. H.; Choi, S. I.
2016-02-01
In this paper, we propose a new/next-generation type of CT examinations, the so-called Interior Computed Tomography (ICT), which may presumably lead to dose reduction to the patient outside the target region-of-interest (ROI), in dental x-ray imaging. Here an x-ray beam from each projection position covers only a relatively small ROI containing a target of diagnosis from the examined structure, leading to imaging benefits such as decreasing scatters and system cost as well as reducing imaging dose. We considered the compressed-sensing (CS) framework, rather than common filtered-backprojection (FBP)-based algorithms, for more accurate ICT reconstruction. We implemented a CS-based ICT algorithm and performed a systematic simulation to investigate the imaging characteristics. Simulation conditions of two ROI ratios of 0.28 and 0.14 between the target and the whole phantom sizes and four projection numbers of 360, 180, 90, and 45 were tested. We successfully reconstructed ICT images of substantially high image quality by using the CS framework even with few-view projection data, still preserving sharp edges in the images.
A computational intelligence approach to the Mars Precision Landing problem
NASA Astrophysics Data System (ADS)
Birge, Brian Kent, III
Various proposed Mars missions, such as the Mars Sample Return Mission (MRSR) and the Mars Smart Lander (MSL), require precise re-entry terminal position and velocity states. This is to achieve mission objectives including rendezvous with a previous landed mission, or reaching a particular geographic landmark. The current state of the art footprint is in the magnitude of kilometers. For this research a Mars Precision Landing is achieved with a landed footprint of no more than 100 meters, for a set of initial entry conditions representing worst guess dispersions. Obstacles to reducing the landed footprint include trajectory dispersions due to initial atmospheric entry conditions (entry angle, parachute deployment height, etc.), environment (wind, atmospheric density, etc.), parachute deployment dynamics, unavoidable injection error (propagated error from launch on), etc. Weather and atmospheric models have been developed. Three descent scenarios have been examined. First, terminal re-entry is achieved via a ballistic parachute with concurrent thrusting events while on the parachute, followed by a gravity turn. Second, terminal re-entry is achieved via a ballistic parachute followed by gravity turn to hover and then thrust vector to desired location. Third, a guided parafoil approach followed by vectored thrusting to reach terminal velocity is examined. The guided parafoil is determined to be the best architecture. The purpose of this study is to examine the feasibility of using a computational intelligence strategy to facilitate precision planetary re-entry, specifically to take an approach that is somewhat more intuitive and less rigid, and see where it leads. The test problems used for all research are variations on proposed Mars landing mission scenarios developed by NASA. A relatively recent method of evolutionary computation is Particle Swarm Optimization (PSO), which can be considered to be in the same general class as Genetic Algorithms. An improvement over
Toward an integrated computational approach to CW-ESR spectra of free radicals.
Barone, Vincenzo; Polimeno, Antonino
2006-10-28
Interpretation of structural properties and dynamic behaviour of molecules in solution is of fundamental importance to understand their stability, chemical reactivity and catalytic action. Information can be gained, in principle, by a variety of spectroscopic techniques, magnetic as well as optical. In particular, continuous wave electron spin resonance (CW-ESR) measurements are highly informative. However, the wealth of structural and dynamic information which can be extracted from ESR spectroscopy is, at present, limited by the necessity of employing computationally efficient models, which are increasingly complex as they need to take into account diverse relaxation processes affecting the spectrum. In this paper, we address the basic theoretical tools needed to predict, essentially ab initio, CW-ESR spectra observables according to the stochastic Liouville equation (SLE) approach, combined with quantum mechanical and hybrid methods for the accurate and efficient computation of structural, spectroscopic and magnetic properties of molecular systems. We shall discuss, on one hand, the quantum mechanical calculation of magnetic observables, via density functional theory (DFT), time-dependent DFT (TD-DFT) and application of the polarizable continuum model (PCM) for the description of environmental effects, including anisotropic environments and systems where different regions are characterized by different dielectric constants. One the other hand, the explicit evaluation of dynamical effects will be discussed based on the numerically exact treatment of the SLE in the presence of several relaxation processes, which has been proven to be a challenging task.
NASA Astrophysics Data System (ADS)
Rybynok, V. O.; Kyriacou, P. A.
2007-10-01
Diabetes is one of the biggest health challenges of the 21st century. The obesity epidemic, sedentary lifestyles and an ageing population mean prevalence of the condition is currently doubling every generation. Diabetes is associated with serious chronic ill health, disability and premature mortality. Long-term complications including heart disease, stroke, blindness, kidney disease and amputations, make the greatest contribution to the costs of diabetes care. Many of these long-term effects could be avoided with earlier, more effective monitoring and treatment. Currently, blood glucose can only be monitored through the use of invasive techniques. To date there is no widely accepted and readily available non-invasive monitoring technique to measure blood glucose despite the many attempts. This paper challenges one of the most difficult non-invasive monitoring techniques, that of blood glucose, and proposes a new novel approach that will enable the accurate, and calibration free estimation of glucose concentration in blood. This approach is based on spectroscopic techniques and a new adaptive modelling scheme. The theoretical implementation and the effectiveness of the adaptive modelling scheme for this application has been described and a detailed mathematical evaluation has been employed to prove that such a scheme has the capability of extracting accurately the concentration of glucose from a complex biological media.
Birnhack, Liat; Sabach, Sara; Lahav, Ori
2012-10-15
A new, simple and accurate method is introduced for determining H(2)CO(3)(*) alkalinity in fresh waters dominated by the carbonate weak-acid system. The method relies on a single H(3)PO(4) dosage and two pH readings (acidic pH value target: pH~4.0). The computation algorithm is based on the concept that the overall alkalinity mass of a solution does not change upon the addition of a non-proton-accepting species. The accuracy of the new method was assessed batch-wise with both synthetic and actual tap waters and the results were compared to those obtained from two widely used alkalinity analysis methods (titration to pH~4.5 and the Gran titration method). The experimental results, which were deliberately obtained with simple laboratory equipment (glass buret, general-purpose pH electrode, magnetic stirrer) proved the method to be as accurate as the conventional methods at a wide range of alkalinity values (20-400 mg L(-1) as CaCO(3)). Analysis of the relative error attained in the proposed method as a function of the target (acidic) pH showed that at the range 4.0
The Computer Connection: Four Approaches to Microcomputer Laboratory Interfacing.
ERIC Educational Resources Information Center
Graef, Jean L.
1983-01-01
Four ways in which microcomputers can be turned into laboratory instruments are discussed. These include adding an analog/digital (A/D) converter on a printed circuit board, adding an external A/D converter using the computer's serial port, attaching transducers to the game paddle ports, or connecting an instrument to the computer. (JN)
Computers and Education: The Wrong Approach Continually Being Executed
ERIC Educational Resources Information Center
Walker, Jacob J.
2005-01-01
This opinion paper explores the use of computers in the U.S. Public Education System, concluding that technology is underutilized and not fulfilled most of the educational promises attributed to the tool. Drawing upon research and personal experience, the paper explores 8 possible reasons for the problem, including: the computer itself; not enough…
Computers and the Humanities Courses: Philosophical Bases and Approach.
ERIC Educational Resources Information Center
Ide, Nancy M.
1987-01-01
Discusses a Vassar College workshop and the debate it generated over the depth and breadth of computer knowledge needed by humanities students. Describes two positions: the "Holistic View," which emphasizes the understanding of the formal methods of computer implementation; and the "Expert Users View," which sees the humanist as a "user" of…
Analysis of Children's Computational Errors: A Qualitative Approach
ERIC Educational Resources Information Center
Engelhardt, J. M.
1977-01-01
This study was designed to replicate and extend Roberts' (1968) efforts at classifying computational errors. 198 elementary school students were administered an 84-item arithmetic computation test. Eight types of errors were described which led to several tentative generalizations. (Editor/RK)
Teaching Computer Science: A Problem Solving Approach that Works.
ERIC Educational Resources Information Center
Allan, V. H.; Kolesar, M. V.
The typical introductory programming course is not an appropriate first computer science course for many students. Initial experiences with programming are often frustrating, resulting in a low rate of successful completion, and focus on syntax rather than providing a representative picture of computer science as a discipline. The paper discusses…
One of the strategic objectives of the Computational Toxicology Program is to develop approaches for prioritizing chemicals for subsequent screening and testing. Approaches currently available for this process require extensive resources. Therefore, less costly and time-extensi...
Accurate Finite Difference Algorithms
NASA Technical Reports Server (NTRS)
Goodrich, John W.
1996-01-01
Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.
What Computational Approaches Should be Taught for Physics?
NASA Astrophysics Data System (ADS)
Landau, Rubin
2005-03-01
The standard Computational Physics courses are designed for upper-level physics majors who already have some computational skills. We believe that it is important for first-year physics students to learn modern computing techniques that will be useful throughout their college careers, even before they have learned the math and science required for Computational Physics. To teach such Introductory Scientific Computing courses requires that some choices be made as to what subjects and computer languages wil be taught. Our survey of colleagues active in Computational Physics and Physics Education show no predominant choice, with strong positions taken for the compiled languages Java, C, C++ and Fortran90, as well as for problem-solving environments like Maple and Mathematica. Over the last seven years we have developed an Introductory course and have written up those courses as text books for others to use. We will describe our model of using both a problem-solving environment and a compiled language. The developed materials are available in both Maple and Mathaematica, and Java and Fortran90ootnotetextPrinceton University Press, to be published; www.physics.orst.edu/˜rubin/IntroBook/.
Mapping Agricultural Fields in Sub-Saharan Africa with a Computer Vision Approach
NASA Astrophysics Data System (ADS)
Debats, S. R.; Luo, D.; Estes, L. D.; Fuchs, T.; Caylor, K. K.
2014-12-01
Sub-Saharan Africa is an important focus for food security research, because it is experiencing unprecedented population growth, agricultural activities are largely dominated by smallholder production, and the region is already home to 25% of the world's undernourished. One of the greatest challenges to monitoring and improving food security in this region is obtaining an accurate accounting of the spatial distribution of agriculture. Households are the primary units of agricultural production in smallholder communities and typically rely on small fields of less than 2 hectares. Field sizes are directly related to household crop productivity, management choices, and adoption of new technologies. As population and agriculture expand, it becomes increasingly important to understand both the distribution of field sizes as well as how agricultural communities are spatially embedded in the landscape. In addition, household surveys, a common tool for tracking agricultural productivity in Sub-Saharan Africa, would greatly benefit from spatially explicit accounting of fields. Current gridded land cover data sets do not provide information on individual agricultural fields or the distribution of field sizes. Therefore, we employ cutting edge approaches from the field of computer vision to map fields across Sub-Saharan Africa, including semantic segmentation, discriminative classifiers, and automatic feature selection. Our approach aims to not only improve the binary classification accuracy of cropland, but also to isolate distinct fields, thereby capturing crucial information on size and geometry. Our research focuses on the development of descriptive features across scales to increase the accuracy and geographic range of our computer vision algorithm. Relevant data sets include high-resolution remote sensing imagery and Landsat (30-m) multi-spectral imagery. Training data for field boundaries is derived from hand-digitized data sets as well as crowdsourcing.
Modeling weakly-ionized plasmas in magnetic field: A new computationally-efficient approach
NASA Astrophysics Data System (ADS)
Parent, Bernard; Macheret, Sergey O.; Shneider, Mikhail N.
2015-11-01
Despite its success at simulating accurately both non-neutral and quasi-neutral weakly-ionized plasmas, the drift-diffusion model has been observed to be a particularly stiff set of equations. Recently, it was demonstrated that the stiffness of the system could be relieved by rewriting the equations such that the potential is obtained from Ohm's law rather than Gauss's law while adding some source terms to the ion transport equation to ensure that Gauss's law is satisfied in non-neutral regions. Although the latter was applicable to multicomponent and multidimensional plasmas, it could not be used for plasmas in which the magnetic field was significant. This paper hence proposes a new computationally-efficient set of electron and ion transport equations that can be used not only for a plasma with multiple types of positive and negative ions, but also for a plasma in magnetic field. Because the proposed set of equations is obtained from the same physical model as the conventional drift-diffusion equations without introducing new assumptions or simplifications, it results in the same exact solution when the grid is refined sufficiently while being more computationally efficient: not only is the proposed approach considerably less stiff and hence requires fewer iterations to reach convergence but it yields a converged solution that exhibits a significantly higher resolution. The combined faster convergence and higher resolution is shown to result in a hundredfold increase in computational efficiency for some typical steady and unsteady plasma problems including non-neutral cathode and anode sheaths as well as quasi-neutral regions.
Methodical Approaches to Teaching of Computer Modeling in Computer Science Course
ERIC Educational Resources Information Center
Rakhimzhanova, B. Lyazzat; Issabayeva, N. Darazha; Khakimova, Tiyshtik; Bolyskhanova, J. Madina
2015-01-01
The purpose of this study was to justify of the formation technique of representation of modeling methodology at computer science lessons. The necessity of studying computer modeling is that the current trends of strengthening of general education and worldview functions of computer science define the necessity of additional research of the…
Reflections on John Monaghan's "Computer Algebra, Instrumentation, and the Anthropological Approach"
ERIC Educational Resources Information Center
Blume, Glen
2007-01-01
Reactions to John Monaghan's "Computer Algebra, Instrumentation and the Anthropological Approach" focus on a variety of issues related to the ergonomic approach (instrumentation) and anthropological approach to mathematical activity and practice. These include uses of the term technique; several possibilities for integration of the two approaches;…
Computational Approaches for Translational Clinical Research in Disease Progression
McGuire, Mary F.; Iyengar, M. Sriram; Mercer, David W.
2011-01-01
Today, there is an ever-increasing amount of biological and clinical data available that could be used to enhance a systems-based understanding of disease progression through innovative computational analysis. In this paper we review a selection of published research regarding computational methodologies, primarily from systems biology, that support translational research from the molecular level to the bedside, with a focus on applications in trauma and critical care. Trauma is the leading cause of mortality in Americans under 45 years of age, and its rapid progression offers both opportunities and challenges for computational analysis of trends in molecular patterns associated with outcomes and therapeutic interventions. This review presents methods and domain-specific examples that may inspire the development of new algorithms and computational methods that utilize both molecular and clinical data for diagnosis, prognosis and therapy in disease progression. PMID:21712727
Reduced-Order Modeling: New Approaches for Computational Physics
NASA Technical Reports Server (NTRS)
Beran, Philip S.; Silva, Walter A.
2001-01-01
In this paper, we review the development of new reduced-order modeling techniques and discuss their applicability to various problems in computational physics. Emphasis is given to methods ba'sed on Volterra series representations and the proper orthogonal decomposition. Results are reported for different nonlinear systems to provide clear examples of the construction and use of reduced-order models, particularly in the multi-disciplinary field of computational aeroelasticity. Unsteady aerodynamic and aeroelastic behaviors of two- dimensional and three-dimensional geometries are described. Large increases in computational efficiency are obtained through the use of reduced-order models, thereby justifying the initial computational expense of constructing these models and inotivatim,- their use for multi-disciplinary design analysis.
An Object-Oriented Approach to Writing Computational Electromagnetics Codes
NASA Technical Reports Server (NTRS)
Zimmerman, Martin; Mallasch, Paul G.
1996-01-01
Presently, most computer software development in the Computational Electromagnetics (CEM) community employs the structured programming paradigm, particularly using the Fortran language. Other segments of the software community began switching to an Object-Oriented Programming (OOP) paradigm in recent years to help ease design and development of highly complex codes. This paper examines design of a time-domain numerical analysis CEM code using the OOP paradigm, comparing OOP code and structured programming code in terms of software maintenance, portability, flexibility, and speed.
AVES: A Computer Cluster System approach for INTEGRAL Scientific Analysis
NASA Astrophysics Data System (ADS)
Federici, M.; Martino, B. L.; Natalucci, L.; Umbertini, P.
The AVES computing system, based on an "Cluster" architecture is a fully integrated, low cost computing facility dedicated to the archiving and analysis of the INTEGRAL data. AVES is a modular system that uses the software resource manager (SLURM) and allows almost unlimited expandibility (65,536 nodes and hundreds of thousands of processors); actually is composed by 30 Personal Computers with Quad-Cores CPU able to reach the computing power of 300 Giga Flops (300x10{9} Floating point Operations Per Second), with 120 GB of RAM and 7.5 Tera Bytes (TB) of storage memory in UFS configuration plus 6 TB for users area. AVES was designed and built to solve growing problems raised from the analysis of the large data amount accumulated by the INTEGRAL mission (actually about 9 TB) and due to increase every year. The used analysis software is the OSA package, distributed by the ISDC in Geneva. This is a very complex package consisting of dozens of programs that can not be converted to parallel computing. To overcome this limitation we developed a series of programs to distribute the workload analysis on the various nodes making AVES automatically divide the analysis in N jobs sent to N cores. This solution thus produces a result similar to that obtained by the parallel computing configuration. In support of this we have developed tools that allow a flexible use of the scientific software and quality control of on-line data storing. The AVES software package is constituted by about 50 specific programs. Thus the whole computing time, compared to that provided by a Personal Computer with single processor, has been enhanced up to a factor 70.
Computational challenges of structure-based approaches applied to HIV.
Forli, Stefano; Olson, Arthur J
2015-01-01
Here, we review some of the opportunities and challenges that we face in computational modeling of HIV therapeutic targets and structural biology, both in terms of methodology development and structure-based drug design (SBDD). Computational methods have provided fundamental support to HIV research since the initial structural studies, helping to unravel details of HIV biology. Computational models have proved to be a powerful tool to analyze and understand the impact of mutations and to overcome their structural and functional influence in drug resistance. With the availability of structural data, in silico experiments have been instrumental in exploiting and improving interactions between drugs and viral targets, such as HIV protease, reverse transcriptase, and integrase. Issues such as viral target dynamics and mutational variability, as well as the role of water and estimates of binding free energy in characterizing ligand interactions, are areas of active computational research. Ever-increasing computational resources and theoretical and algorithmic advances have played a significant role in progress to date, and we envision a continually expanding role for computational methods in our understanding of HIV biology and SBDD in the future.
The Future of Computer-Based Toxicity Prediction:
Mechanism-Based Models vs. Information Mining Approaches
When we speak of computer-based toxicity prediction, we are generally referring to a broad array of approaches which rely primarily upon chemical structure ...
Computer Mediated Learning: An Example of an Approach.
ERIC Educational Resources Information Center
Arcavi, Abraham; Hadas, Nurit
2000-01-01
There are several possible approaches in which dynamic computerized environments play a significant and possibly unique role in supporting innovative learning trajectories in mathematics in general and geometry in particular. Describes an approach based on a problem situation and some experiences using it with students and teachers. (Contains 15…
NASA Technical Reports Server (NTRS)
Schwenke, David W.; Mladenovic, Mirjana; Zhao, Meishan; Truhlar, Donald G.; Sun, Yan
1988-01-01
The computational steps in calculating quantum mechanical reactive scattering amplitudes by the L2 generalized Newton variational principle are discussed with emphasis on computational strategies and recent improvements that make the calculations more efficient. Special emphasis is placed on quadrature techniques, storage management strategies, use of symmetry, and boundary conditions. It is concluded that an efficient implementation of these procedures provides a powerful algorithm for the accurate solution of the Schroedinger equation for rearrangements.
A Computational Approach to Qualitative Analysis in Large Textual Datasets
Evans, Michael S.
2014-01-01
In this paper I introduce computational techniques to extend qualitative analysis into the study of large textual datasets. I demonstrate these techniques by using probabilistic topic modeling to analyze a broad sample of 14,952 documents published in major American newspapers from 1980 through 2012. I show how computational data mining techniques can identify and evaluate the significance of qualitatively distinct subjects of discussion across a wide range of public discourse. I also show how examining large textual datasets with computational methods can overcome methodological limitations of conventional qualitative methods, such as how to measure the impact of particular cases on broader discourse, how to validate substantive inferences from small samples of textual data, and how to determine if identified cases are part of a consistent temporal pattern. PMID:24498398
A computational approach to qualitative analysis in large textual datasets.
Evans, Michael S
2014-01-01
In this paper I introduce computational techniques to extend qualitative analysis into the study of large textual datasets. I demonstrate these techniques by using probabilistic topic modeling to analyze a broad sample of 14,952 documents published in major American newspapers from 1980 through 2012. I show how computational data mining techniques can identify and evaluate the significance of qualitatively distinct subjects of discussion across a wide range of public discourse. I also show how examining large textual datasets with computational methods can overcome methodological limitations of conventional qualitative methods, such as how to measure the impact of particular cases on broader discourse, how to validate substantive inferences from small samples of textual data, and how to determine if identified cases are part of a consistent temporal pattern.
Artificial Intelligence Approaches to Computer-Based Instruction.
ERIC Educational Resources Information Center
Bregar, William S.; Farley, Arthur M.
1980-01-01
Explores how new, operational models of cognition processing developed in Artificial Intelligence (AI) can be applied in computer assisted instruction (CAI) systems. CAI systems are surveyed in terms of their goals and formalisms, and a model for the development of a tutorial CAI system for algebra problem solving is introduced. (Author)
A "Service-Learning Approach" to Teaching Computer Graphics
ERIC Educational Resources Information Center
Hutzel, Karen
2007-01-01
The author taught a computer graphics course through a service-learning framework to undergraduate and graduate students in the spring of 2003 at Florida State University (FSU). The students in this course participated in learning a software program along with youths from a neighboring, low-income, primarily African-American community. Together,…
Preparing Students for Computer Aided Drafting (CAD). A Conceptual Approach.
ERIC Educational Resources Information Center
Putnam, A. R.; Duelm, Brian
This presentation outlines guidelines for developing and implementing an introductory course in computer-aided drafting (CAD) that is geared toward secondary-level students. The first section of the paper, which deals with content identification and selection, includes lists of mechanical drawing and CAD competencies and a list of rationales for…
A Computer-Assisted Instructional Approach to Teaching Applied Therapeutics.
ERIC Educational Resources Information Center
Jim, Lucia K.; And Others
1984-01-01
The effectiveness of computer-assisted instruction to conduct pharmacy therapeutics case analysis exercises was compared with the traditional conference format. Pre- and posttest scores were compared statistically within and between groups to determine knowledge gained and comparative effectivness of teaching. (Author/MLW)
Lattice algebra approach to single-neuron computation.
Ritter, G X; Urcid, G
2003-01-01
Recent advances in the biophysics of computation and neurocomputing models have brought to the foreground the importance of dendritic structures in a single neuron cell. Dendritic structures are now viewed as the primary autonomous computational units capable of realizing logical operations. By changing the classic simplified model of a single neuron with a more realistic one that incorporates the dendritic processes, a novel paradigm in artificial neural networks is being established. In this work, we introduce and develop a mathematical model of dendrite computation in a morphological neuron based on lattice algebra. The computational capabilities of this enriched neuron model are demonstrated by means of several illustrative examples and by proving that any single layer morphological perceptron endowed with dendrites and their corresponding input and output synaptic processes is able to approximate any compact region in higher dimensional Euclidean space to within any desired degree of accuracy. Based on this result, we describe a training algorithm for single layer morphological perceptrons and apply it to some well-known nonlinear problems in order to exhibit its performance.
Linguistics, Computers, and the Language Teacher. A Communicative Approach.
ERIC Educational Resources Information Center
Underwood, John H.
This analysis of the state of the art of computer programs and programming for language teaching has two parts. In the first part, an overview of the theory and practice of language teaching, Noam Chomsky's view of language, and the implications and problems of generative theory are presented. The theory behind the input model of language…
Multiple von Neumann computers: an evolutionary approach to functional emergence.
Suzuki, H
1997-01-01
A novel system composed of multiple von Neumann computers and an appropriate problem environment is proposed and simulated. Each computer has a memory to store the machine instruction program, and when a program is executed, a series of machine codes in the memory is sequentially decoded, leading to register operations in the central processing unit (CPU). By means of these operations, the computer not only can handle its generally used registers but also can read and write the environmental database. Simulation is driven by genetic algorithms (GAs) performed on the population of program memories. Mutation and crossover create program diversity in the memory, and selection facilitates the reproduction of appropriate programs. Through these evolutionary operations, advantageous combinations of machine codes are created and fixed in the population one by one, and the higher function, which enables the computer to calculate an appropriate number from the environment, finally emerges in the program memory. In the latter half of the article, the performance of GAs on this system is studied. Under different sets of parameters, the evolutionary speed, which is determined by the time until the domination of the final program, is examined and the conditions for faster evolution are clarified. At an intermediate mutation rate and at an intermediate population size, crossover helps create novel advantageous sets of machine codes and evidently accelerates optimization by GAs.
A New Approach: Computer-Assisted Problem-Solving Systems
ERIC Educational Resources Information Center
Gok, Tolga
2010-01-01
Computer-assisted problem solving systems are rapidly growing in educational use and with the advent of the Internet. These systems allow students to do their homework and solve problems online with the help of programs like Blackboard, WebAssign and LON-CAPA program etc. There are benefits and drawbacks of these systems. In this study, the…
Traditional versus Computer-Mediated Approaches of Teaching Educational Measurement
ERIC Educational Resources Information Center
Alkharusi, Hussain; Kazem, Ali; Al-Musawai, Ali
2010-01-01
Research suggests that to adequately prepare teachers for the task of classroom assessment, attention should be given to the educational measurement instruction. In addition, the literature indicates that the use of computer-mediated instruction has the potential to affect student knowledge, skills, and attitudes. This study compared the effects…
An Interdisciplinary, Computer-Centered Approach to Active Learning.
ERIC Educational Resources Information Center
Misale, Judi M.; And Others
1996-01-01
Describes a computer-assisted, interdisciplinary course in decision making developed to promote student participation and critical thinking. Students participate in 20 interactive exercises that utilize and illustrate psychological and economic concepts. Follow-up activities include receiving background information, group discussions, text…
Computational Modelling and Simulation Fostering New Approaches in Learning Probability
ERIC Educational Resources Information Center
Kuhn, Markus; Hoppe, Ulrich; Lingnau, Andreas; Wichmann, Astrid
2006-01-01
Discovery learning in mathematics in the domain of probability based on hands-on experiments is normally limited because of the difficulty in providing sufficient materials and data volume in terms of repetitions of the experiments. Our cooperative, computational modelling and simulation environment engages students and teachers in composing and…
Computer-Assisted Mathematics--A Model Approach.
ERIC Educational Resources Information Center
Bitter, Gary G.
1987-01-01
Discussion of need for improved mathematics education of preservice teachers focuses on a model program, the Mathematics Fitness Project, that includes a computer-generated testing system, management system, and remediation system. Use of the system to improve mathematics skills and attitudes of college students and post high school adults is…
A Functional Analytic Approach to Computer-Interactive Mathematics
ERIC Educational Resources Information Center
Ninness, Chris; Rumph, Robin; McCuller, Glen; Harrison, Carol; Ford, Angela M.; Ninness, Sharon K.
2005-01-01
Following a pretest, 11 participants who were naive with regard to various algebraic and trigonometric transformations received an introductory lecture regarding the fundamentals of the rectangular coordinate system. Following the lecture, they took part in a computer-interactive matching-to-sample procedure in which they received training on…
Countering Deterministic Tools: A Critical Theory Approach to Computers & Composition.
ERIC Educational Resources Information Center
Kimme Hea, Amy C.
A writing instructor has grappled with how both to integrate and to complicate critical perspectives on technology in the writing classroom. In collaboration with another instructor, a computer classroom pedagogy was constructed emphasizing imperatives of cultural studies practice as outlined by James Berlin. The pedagogy is similar to Berlin's…
An algebraic approach to computer program design and memory management
NASA Astrophysics Data System (ADS)
Raynolds, James; Mullin, Lenore
2008-03-01
Beginning with an algebra of multi-dimensional arrays and following a set of reduction rules embodying a calculus of array indices, we translate (in a mechanizable way) from the high-level mathematics of any array-based problem and a machine specification to a mathematically-optimized implementation. Raynolds and Mullin introduced the name Conformal Computing,^to describe this process that will be discussed in the context of data transforms such as the Fast Fourier, Wavelet Transforms and QR decomposition. We discuss the discovery that the access patterns of the Wavelet Transform form a sufficiently regular subset of those for our cache-optimized FFT so that we can be assured of achieving similar efficiency improvements to the Wavelet Transform as those that were found for the FFT. We present recent results in which careful attention to reproducible computational experiments in a dedicated/non-shared environment is demonstrated to be essential in order to optimally measure the response of the system (in this case the computer itself is the object of study) so as to be able to optimally tune the algorithm to the numerous cost functions associated with all of the elements of the memory/disk/network hierarchy. ^ The name Conformal Computing is protected: 2003, The Research Foundation, State University of New York.
Several Approaches to a Basic Problem in Computer Graphics.
ERIC Educational Resources Information Center
Smart, James R.
1988-01-01
Considers the problem of how to go from three coordinates to two. States that it is not a problem that mathematics students ordinarily encounter. Presents four methods of graphing three-dimensional figures on a two-dimensional computer screen. (PK)
The Cognitive Approach to Computer Courseware Design and Evaluation.
ERIC Educational Resources Information Center
Jay, Timothy B.
1983-01-01
Focuses on five human information processing abilities which cognitive psychologists anticipate must be accounted for in order to develop good computer courseware--memory and attention; language or text characteristics; graphics and visual processing; cognitive characteristics of user; feedback to users. A 31-item bibliography is included. (EJS)
Liu, Aiping; Li, Junning; Wang, Z. Jane; McKeown, Martin J.
2012-01-01
Graphical models appear well suited for inferring brain connectivity from fMRI data, as they can distinguish between direct and indirect brain connectivity. Nevertheless, biological interpretation requires not only that the multivariate time series are adequately modeled, but also that there is accurate error-control of the inferred edges. The PCfdr algorithm, which was developed by Li and Wang, was to provide a computationally efficient means to control the false discovery rate (FDR) of computed edges asymptotically. The original PCfdr algorithm was unable to accommodate a priori information about connectivity and was designed to infer connectivity from a single subject rather than a group of subjects. Here we extend the original PCfdr algorithm and propose a multisubject, error-rate-controlled brain connectivity modeling approach that allows incorporation of prior knowledge of connectivity. In simulations, we show that the two proposed extensions can still control the FDR around or below a specified threshold. When the proposed approach is applied to fMRI data in a Parkinson's disease study, we find robust group evidence of the disease-related changes, the compensatory changes, and the normalizing effect of L-dopa medication. The proposed method provides a robust, accurate, and practical method for the assessment of brain connectivity patterns from functional neuroimaging data. PMID:23251232
ERIC Educational Resources Information Center
Zajenkowski, Marcin; Styla, Rafal; Szymanik, Jakub
2011-01-01
We compared the processing of natural language quantifiers in a group of patients with schizophrenia and a healthy control group. In both groups, the difficulty of the quantifiers was consistent with computational predictions, and patients with schizophrenia took more time to solve the problems. However, they were significantly less accurate only…
James, Conrad D.; Schiess, Adrian B.; Howell, Jamie; Baca, Michael J.; Partridge, L. Donald; Finnegan, Patrick Sean; Wolfley, Steven L.; Dagel, Daryl James; Spahn, Olga Blum; Harper, Jason C.; Pohl, Kenneth Roy; Mickel, Patrick R.; Lohn, Andrew; Marinella, Matthew
2013-10-01
The human brain (volume=1200cm3) consumes 20W and is capable of performing > 10^16 operations/s. Current supercomputer technology has reached 1015 operations/s, yet it requires 1500m^3 and 3MW, giving the brain a 10^12 advantage in operations/s/W/cm^3. Thus, to reach exascale computation, two achievements are required: 1) improved understanding of computation in biological tissue, and 2) a paradigm shift towards neuromorphic computing where hardware circuits mimic properties of neural tissue. To address 1), we will interrogate corticostriatal networks in mouse brain tissue slices, specifically with regard to their frequency filtering capabilities as a function of input stimulus. To address 2), we will instantiate biological computing characteristics such as multi-bit storage into hardware devices with future computational and memory applications. Resistive memory devices will be modeled, designed, and fabricated in the MESA facility in consultation with our internal and external collaborators.
Computing pKa Values with a Mixing Hamiltonian Quantum Mechanical/Molecular Mechanical Approach.
Liu, Yang; Fan, Xiaoli; Jin, Yingdi; Hu, Xiangqian; Hu, Hao
2013-09-10
Accurate computation of the pKa value of a compound in solution is important but challenging. Here, a new mixing quantum mechanical/molecular mechanical (QM/MM) Hamiltonian method is developed to simulate the free-energy change associated with the protonation/deprotonation processes in solution. The mixing Hamiltonian method is designed for efficient quantum mechanical free-energy simulations by alchemically varying the nuclear potential, i.e., the nuclear charge of the transforming nucleus. In pKa calculation, the charge on the proton is varied in fraction between 0 and 1, corresponding to the fully deprotonated and protonated states, respectively. Inspired by the mixing potential QM/MM free energy simulation method developed previously [H. Hu and W. T. Yang, J. Chem. Phys. 2005, 123, 041102], this method succeeds many advantages of a large class of λ-coupled free-energy simulation methods and the linear combination of atomic potential approach. Theory and technique details of this method, along with the calculation results of the pKa of methanol and methanethiol molecules in aqueous solution, are reported. The results show satisfactory agreement with the experimental data.
Design of New and Potent Diethyl Thiobarbiturates as Urease Inhibitors: A Computational Approach
Wadood, Abdul; Riaz, Muhammad; Mulk, Amir ul; Khan, Momin; Haleem, Sobia Ahsan; Shams, Sulaiman; Gul, Sahib; Ahmed, Ayaz; Qasim, Muhammad; Ali, Farman; Ul-Haq, Zaheer
2014-01-01
Urease is an important enzyme both in agriculture and medicine research. Strategies based on urease inhibition is critically considered as the first line treatment of infections caused by urease producing bacteria. Since, urease possess agro-chemical and medicinal importance, thus, it is necessary to search for the novel compounds capable of inhibiting this enzyme. Several computational methods were employed to design novel and potent urease inhibitors in this work. First docking simulations of known compounds consists of a set of arylidine barbiturates (termed as reference) were performed on the Bacillus pasteurii (BP) urease. Subsequently, two fold strategies were used to design new compounds against urease. Stage 1 comprised of the energy minimization of enzyme-ligand complexes of reference compounds and the accurate prediction of the molecular mechanics generalized born (MMGB) interaction energies. In the second stage, new urease inhibitors were then designed by the substitution of different groups consecutively in the aryl ring of the thiobarbiturates and N, N-diethyl thiobarbiturates of the reference ligands.. The enzyme-ligand complexes with lowest interaction energies or energies close to the calculated interaction energies of the reference molecules, were selected for the consequent chemical manipulation. This was followed by the substitution of different groups on the 2 and 5 positions of the aryl ring. As a result, several new and potent diethyl thiobarbiturates were predicted as urease inhibitors. This approach reflects a logical progression for early stage drug discovery that can be exploited to successfully identify potential drug candidates. PMID:24966538
Design of new and potent diethyl thiobarbiturates as urease inhibitors: a computational approach.
Wadood, Abdul; Riaz, Muhammad; Mulk, Amir Ul; Khan, Momin; Haleem, Sobia Ahsan; Shams, Sulaiman; Gul, Sahib; Ahmed, Ayaz; Qasim, Muhammad; Ali, Farman; Ul-Haq, Zaheer
2014-01-01
Urease is an important enzyme both in agriculture and medicine research. Strategies based on urease inhibition is critically considered as the first line treatment of infections caused by urease producing bacteria. Since, urease possess agro-chemical and medicinal importance, thus, it is necessary to search for the novel compounds capable of inhibiting this enzyme. Several computational methods were employed to design novel and potent urease inhibitors in this work. First docking simulations of known compounds consists of a set of arylidine barbiturates (termed as reference) were performed on the Bacillus pasteurii (BP) urease. Subsequently, two fold strategies were used to design new compounds against urease. Stage 1 comprised of the energy minimization of enzyme-ligand complexes of reference compounds and the accurate prediction of the molecular mechanics generalized born (MMGB) interaction energies. In the second stage, new urease inhibitors were then designed by the substitution of different groups consecutively in the aryl ring of the thiobarbiturates and N, N-diethyl thiobarbiturates of the reference ligands.. The enzyme-ligand complexes with lowest interaction energies or energies close to the calculated interaction energies of the reference molecules, were selected for the consequent chemical manipulation. This was followed by the substitution of different groups on the 2 and 5 positions of the aryl ring. As a result, several new and potent diethyl thiobarbiturates were predicted as urease inhibitors. This approach reflects a logical progression for early stage drug discovery that can be exploited to successfully identify potential drug candidates. PMID:24966538
Monti, Susanna; Prampolini, Giacomo; Barone, Vincenzo
2015-01-01
The spectroscopic properties of the organic chromophore 4-naphthoyloxy-1-methoxy-2,2,6,6-tetramethylpiperidine (NfO-TEMPO-Me) in toluene solution are explored through an integrated computational strategy combining a classical dynamic sampling with a quantum mechanical description within the framework of the time-dependent density functional theory (TDDFT) approach. The atomistic simulations are based on an accurately parametrized force field, specifically designed to represent the conformational behavior of the molecule in its ground and bright excited states, whereas TDDFT calculations are performed through a selected combination of hybrid functionals and basis sets to obtain optical spectra closely matching the experimental findings. Solvent effects, crucial to obtain good accuracy, are taken into account through explicit molecules and polarizable continuum descriptions. Although, in the case of toluene, specific solvation is not fundamental, the detailed conformational sampling in solution has confirmed the importance of a dynamic description of the molecular geometry for a reliable description of the photophysical properties of the dye. The agreement between theoretical and experimental data is established and a robust protocol for the prediction of the optical behaviour of flexible fluorophores in solution is set. PMID:26504457
Boitard, Simon; Rodríguez, Willy; Jay, Flora; Mona, Stefano; Austerlitz, Frédéric
2016-01-01
Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey), PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles. PMID:26943927
Boitard, Simon; Rodríguez, Willy; Jay, Flora; Mona, Stefano; Austerlitz, Frédéric
2016-03-01
Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey), PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles.
TOWARD HIGHLY SECURE AND AUTONOMIC COMPUTING SYSTEMS: A HIERARCHICAL APPROACH
Lee, Hsien-Hsin S
2010-05-11
The overall objective of this research project is to develop novel architectural techniques as well as system software to achieve a highly secure and intrusion-tolerant computing system. Such system will be autonomous, self-adapting, introspective, with self-healing capability under the circumstances of improper operations, abnormal workloads, and malicious attacks. The scope of this research includes: (1) System-wide, unified introspection techniques for autonomic systems, (2) Secure information-flow microarchitecture, (3) Memory-centric security architecture, (4) Authentication control and its implication to security, (5) Digital right management, (5) Microarchitectural denial-of-service attacks on shared resources. During the period of the project, we developed several architectural techniques and system software for achieving a robust, secure, and reliable computing system toward our goal.
Analytic reconstruction approach for parallel translational computed tomography.
Kong, Huihua; Yu, Hengyong
2015-01-01
To develop low-cost and low-dose computed tomography (CT) scanners for developing countries, recently a parallel translational computed tomography (PTCT) is proposed, and the source and detector are translated oppositely with respect to the imaging object without a slip-ring. In this paper, we develop an analytic filtered-backprojection (FBP)-type reconstruction algorithm for two dimensional (2D) fan-beam PTCT and extend it to three dimensional (3D) cone-beam geometry in a Feldkamp-type framework. Particularly, a weighting function is constructed to deal with data redundancy for multiple translations PTCT to eliminate image artifacts. Extensive numerical simulations are performed to validate and evaluate the proposed analytic reconstruction algorithms, and the results confirm their correctness and merits. PMID:25882732
Koutkias, Vassilis G; Jaulent, Marie-Christine
2015-03-01
Computational signal detection constitutes a key element of postmarketing drug monitoring and surveillance. Diverse data sources are considered within the 'search space' of pharmacovigilance scientists, and respective data analysis methods are employed, all with their qualities and shortcomings, towards more timely and accurate signal detection. Recent systematic comparative studies highlighted not only event-based and data-source-based differential performance across methods but also their complementarity. These findings reinforce the arguments for exploiting all possible information sources for drug safety and the parallel use of multiple signal detection methods. Combinatorial signal detection has been pursued in few studies up to now, employing a rather limited number of methods and data sources but illustrating well-promising outcomes. However, the large-scale realization of this approach requires systematic frameworks to address the challenges of the concurrent analysis setting. In this paper, we argue that semantic technologies provide the means to address some of these challenges, and we particularly highlight their contribution in (a) annotating data sources and analysis methods with quality attributes to facilitate their selection given the analysis scope; (b) consistently defining study parameters such as health outcomes and drugs of interest, and providing guidance for study setup; (c) expressing analysis outcomes in a common format enabling data sharing and systematic comparisons; and (d) assessing/supporting the novelty of the aggregated outcomes through access to reference knowledge sources related to drug safety. A semantically-enriched framework can facilitate seamless access and use of different data sources and computational methods in an integrated fashion, bringing a new perspective for large-scale, knowledge-intensive signal detection.
Computational Approaches to Viral Evolution and Rational Vaccine Design
NASA Astrophysics Data System (ADS)
Bhattacharya, Tanmoy
2006-10-01
Viral pandemics, including HIV, are a major health concern across the world. Experimental techniques available today have uncovered a great wealth of information about how these viruses infect, grow, and cause disease; as well as how our body attempts to defend itself against them. Nevertheless, due to the high variability and fast evolution of many of these viruses, the traditional method of developing vaccines by presenting a heuristically chosen strain to the body fails and an effective intervention strategy still eludes us. A large amount of carefully curated genomic data on a number of these viruses are now available, often annotated with disease and immunological context. The availability of parallel computers has now made it possible to carry out a systematic analysis of this data within an evolutionary framework. I will describe, as an example, how computations on such data has allowed us to understand the origins and diversification of HIV, the causative agent of AIDS. On the practical side, computations on the same data is now being used to inform choice or defign of optimal vaccine strains.
Modeling Cu2+-Aβ complexes from computational approaches
NASA Astrophysics Data System (ADS)
Alí-Torres, Jorge; Mirats, Andrea; Maréchal, Jean-Didier; Rodríguez-Santiago, Luis; Sodupe, Mariona
2015-09-01
Amyloid plaques formation and oxidative stress are two key events in the pathology of the Alzheimer disease (AD), in which metal cations have been shown to play an important role. In particular, the interaction of the redox active Cu2+ metal cation with Aβ has been found to interfere in amyloid aggregation and to lead to reactive oxygen species (ROS). A detailed knowledge of the electronic and molecular structure of Cu2+-Aβ complexes is thus important to get a better understanding of the role of these complexes in the development and progression of the AD disease. The computational treatment of these systems requires a combination of several available computational methodologies, because two fundamental aspects have to be addressed: the metal coordination sphere and the conformation adopted by the peptide upon copper binding. In this paper we review the main computational strategies used to deal with the Cu2+-Aβ coordination and build plausible Cu2+-Aβ models that will afterwards allow determining physicochemical properties of interest, such as their redox potential.
Computational Approach to Diarylprolinol-Silyl Ethers in Aminocatalysis.
Halskov, Kim Søholm; Donslund, Bjarke S; Paz, Bruno Matos; Jørgensen, Karl Anker
2016-05-17
Asymmetric organocatalysis has witnessed a remarkable development since its "re-birth" in the beginning of the millenium. In this rapidly growing field, computational investigations have proven to be an important contribution for the elucidation of mechanisms and rationalizations of the stereochemical outcomes of many of the reaction concepts developed. The improved understanding of mechanistic details has facilitated the further advancement of the field. The diarylprolinol-silyl ethers have since their introduction been one of the most applied catalysts in asymmetric aminocatalysis due to their robustness and generality. Although aminocatalytic methods at first glance appear to follow relatively simple mechanistic principles, more comprehensive computational studies have shown that this notion in some cases is deceiving and that more complex pathways might be operating. In this Account, the application of density functional theory (DFT) and other computational methods on systems catalyzed by the diarylprolinol-silyl ethers is described. It will be illustrated how computational investigations have shed light on the structure and reactivity of important intermediates in aminocatalysis, such as enamines and iminium ions formed from aldehydes and α,β-unsaturated aldehydes, respectively. Enamine and iminium ion catalysis can be classified as HOMO-raising and LUMO-lowering activation modes. In these systems, the exclusive reactivity through one of the possible intermediates is often a requisite for achieving high stereoselectivity; therefore, the appreciation of subtle energy differences has been vital for the efficient development of new stereoselective reactions. The diarylprolinol-silyl ethers have also allowed for novel activation modes for unsaturated aldehydes, which have opened up avenues for the development of new remote functionalization reactions of poly-unsaturated carbonyl compounds via di-, tri-, and tetraenamine intermediates and vinylogous iminium ions
Component-based approach to robot vision for computational efficiency
NASA Astrophysics Data System (ADS)
Lee, Junhee; Kim, Dongsun; Park, Yeonchool; Park, Sooyong; Lee, Sukhan
2007-12-01
The purpose of this paper is to show merit and feasibility of the component based approach in robot system integration. Many methodologies such as 'component based approach, 'middle ware based approach' are suggested to integrate various complex functions on robot system efficiently. However, these methodologies are not used to robot function development broadly, because these 'Top-down' methodologies are modeled and researched in software engineering field, which are different from robot function researches, so that cannot be trusted by function developers. Developers' the main concern of these methodologies is the performance decreasing, which origins from overhead of a framework. This paper overcomes this misunderstanding by showing time performance increasing, when an experiment uses 'Self Healing, Adaptive and Growing softwarE (SHAGE)' framework, one of the component based framework. As an example of real robot function, visual object recognition is chosen to experiment.
Computational approach for calculating bound states in quantum field theory
NASA Astrophysics Data System (ADS)
Lv, Q. Z.; Norris, S.; Brennan, R.; Stefanovich, E.; Su, Q.; Grobe, R.
2016-09-01
We propose a nonperturbative approach to calculate bound-state energies and wave functions for quantum field theoretical models. It is based on the direct diagonalization of the corresponding quantum field theoretical Hamiltonian in an effectively discretized and truncated Hilbert space. We illustrate this approach for a Yukawa-like interaction between fermions and bosons in one spatial dimension and show where it agrees with the traditional method based on the potential picture and where it deviates due to recoil and radiative corrections. This method permits us also to obtain some insight into the spatial characteristics of the distribution of the fermions in the ground state, such as the bremsstrahlung-induced widening.
Workflow Scheduling in Grid Computing Environment using a Hybrid GAACO Approach
NASA Astrophysics Data System (ADS)
Sathish, Kuppani; RamaMohan Reddy, A.
2016-06-01
In recent trends, grid computing is one of the emerging areas in computing platform which supports parallel and distributed environments. The main problem for grid computing is scheduling of workflows in terms of user specifications is a stimulating task and it also impacts the performance. This paper proposes a hybrid GAACO approach, which is a combination of Genetic Algorithm and Ant Colony Optimization Algorithm. The GAACO approach proposes different types of scheduling heuristics for the grid environment. The main objective of this approach is to satisfy all the defined constraints and user parameters.
Computational approaches to metabolic engineering utilizing systems biology and synthetic biology.
Fong, Stephen S
2014-08-01
Metabolic engineering modifies cellular function to address various biochemical applications. Underlying metabolic engineering efforts are a host of tools and knowledge that are integrated to enable successful outcomes. Concurrent development of computational and experimental tools has enabled different approaches to metabolic engineering. One approach is to leverage knowledge and computational tools to prospectively predict designs to achieve the desired outcome. An alternative approach is to utilize combinatorial experimental tools to empirically explore the range of cellular function and to screen for desired traits. This mini-review focuses on computational systems biology and synthetic biology tools that can be used in combination for prospective in silico strain design.
One Approach to Computer Modeling of Microkinetics for Biotechnological Processes
NASA Astrophysics Data System (ADS)
Kabiljanov, A. S.; Fozilova, M. M.; Kuchkarov, F. S.
Intelligence — algorithmic method of modeling of microkinetics for biotechnological processes (BTP) is considered. The generalized mathematical model of microkinetics of biotechnological processes received on the basis of the system approach is given. The question of regularization of a task of parametrical identification is considered.
Synergy between experimental and computational approaches to homogeneous photoredox catalysis.
Demissie, Taye B; Hansen, Jørn H
2016-07-01
In this Frontiers article, we highlight how state-of-the-art density functional theory calculations can contribute to the field of homogeneous photoredox catalysis. We discuss challenges in the fields and potential solutions to be found at the interface between theory and experiment. The exciting opportunities and insights that can arise through such an interdisciplinary approach are highlighted.
The effective molarity (EM)--a computational approach.
Karaman, Rafik
2010-08-01
The effective molarity (EM) for 12 intramolecular S(N)2 processes involving the formation of substituted aziridines and substituted epoxides were computed using ab initio and DFT calculation methods. Strong correlation was found between the calculated effective molarity and the experimentally determined values. This result could open a door for obtaining EM values for intramolecular processes that are difficult to be experimentally provided. Furthermore, the calculation results reveal that the driving forces for ring-closing reactions in the two different systems are proximity orientation of the nucleophile to the electrophile and the ground strain energies of the products and the reactants.
New approaches for computer analysis of nucleic acid sequences.
Karlin, S; Ghandour, G; Ost, F; Tavare, S; Korn, L J
1983-09-01
A new high-speed computer algorithm is outlined that ascertains within and between nucleic acid and protein sequences all direct repeats, dyad symmetries, and other structural relationships. Large repeats, repeats of high frequency, dyad symmetries of specified stem length and loop distance, and their distributions are determined. Significance of homologies is assessed by a hierarchy of permutation procedures. Applications are made to papovaviruses, the human papillomavirus HPV, lambda phage, the human and mouse mitochondrial genomes, and the human and mouse immunoglobulin kappa-chain genes. PMID:6577449
A complex systems approach to computational molecular biology
Lapedes, A. |
1993-09-01
We report on the containing research program at Santa Fe Institute that applies complex systems methodology to computational molecular biology. Two aspects are stressed here are the use of co-evolving adaptive neutral networks for determining predictable protein structure classifications, and the use of information theory to elucidate protein structure and function. A ``snapshot`` of the current state of research in these two topics is presented, representing the present state of two major research thrusts in the program of Genetic Data and Sequence Analysis at the Santa Fe Institute.
A computer simulation approach to measurement of human control strategy
NASA Technical Reports Server (NTRS)
Green, J.; Davenport, E. L.; Engler, H. F.; Sears, W. E., III
1982-01-01
Human control strategy is measured through use of a psychologically-based computer simulation which reflects a broader theory of control behavior. The simulation is called the human operator performance emulator, or HOPE. HOPE was designed to emulate control learning in a one-dimensional preview tracking task and to measure control strategy in that setting. When given a numerical representation of a track and information about current position in relation to that track, HOPE generates positions for a stick controlling the cursor to be moved along the track. In other words, HOPE generates control stick behavior corresponding to that which might be used by a person learning preview tracking.
Computational Approaches to Enhance Nanosafety and Advance Nanomedicine
NASA Astrophysics Data System (ADS)
Mendoza, Eduardo R.
With the increasing use of nanoparticles in food processing, filtration/purification and consumer products, as well as the huge potential of their use in nanomedicine, a quantitative understanding of the effects of nanoparticle uptake and transport is needed. We provide examples of novel methods for modeling complex bio-nano interactions which are based on stochastic process algebras. Since model construction presumes sufficient availability of experimental data, recent developments in "nanoinformatics", an emerging discipline analogous to bioinfomatics, in building an accessible information infrastructure are subsequently discussed. Both computational areas offer opportunities for Filipinos to engage in collaborative, cutting edge research in this impactful field.
Cognitive control in majority search: a computational modeling approach.
Wang, Hongbin; Liu, Xun; Fan, Jin
2011-01-01
Despite the importance of cognitive control in many cognitive tasks involving uncertainty, the computational mechanisms of cognitive control in response to uncertainty remain unclear. In this study, we develop biologically realistic neural network models to investigate the instantiation of cognitive control in a majority function task, where one determines the category to which the majority of items in a group belong. Two models are constructed, both of which include the same set of modules representing task-relevant brain functions and share the same model structure. However, with a critical change of a model parameter setting, the two models implement two different underlying algorithms: one for grouping search (where a subgroup of items are sampled and re-sampled until a congruent sample is found) and the other for self-terminating search (where the items are scanned and counted one-by-one until the majority is decided). The two algorithms hold distinct implications for the involvement of cognitive control. The modeling results show that while both models are able to perform the task, the grouping search model fit the human data better than the self-terminating search model. An examination of the dynamics underlying model performance reveals how cognitive control might be instantiated in the brain for computing the majority function.
Computational Approaches to Toll-Like Receptor 4 Modulation.
Billod, Jean-Marc; Lacetera, Alessandra; Guzmán-Caldentey, Joan; Martín-Santamaría, Sonsoles
2016-01-01
Toll-like receptor 4 (TLR4), along with its accessory protein myeloid differentiation factor 2 (MD-2), builds a heterodimeric complex that specifically recognizes lipopolysaccharides (LPS), which are present on the cell wall of Gram-negative bacteria, activating the innate immune response. Some TLR4 modulators are undergoing preclinical and clinical evaluation for the treatment of sepsis, inflammatory diseases, cancer and rheumatoid arthritis. Since the relatively recent elucidation of the X-ray crystallographic structure of the extracellular domain of TLR4, research around this fascinating receptor has risen to a new level, and thus, new perspectives have been opened. In particular, diverse computational techniques have been applied to decipher some of the basis at the atomic level regarding the mechanism of functioning and the ligand recognition processes involving the TLR4/MD-2 system at the atomic level. This review summarizes the reported molecular modeling and computational studies that have recently provided insights into the mechanism regulating the activation/inactivation of the TLR4/MD-2 system receptor and the key interactions modulating the molecular recognition process by agonist and antagonist ligands. These studies have contributed to the design and the discovery of novel small molecules with promising activity as TLR4 modulators. PMID:27483231
Computational approaches for inferring the functions of intrinsically disordered proteins
Varadi, Mihaly; Vranken, Wim; Guharoy, Mainak; Tompa, Peter
2015-01-01
Intrinsically disordered proteins (IDPs) are ubiquitously involved in cellular processes and often implicated in human pathological conditions. The critical biological roles of these proteins, despite not adopting a well-defined fold, encouraged structural biologists to revisit their views on the protein structure-function paradigm. Unfortunately, investigating the characteristics and describing the structural behavior of IDPs is far from trivial, and inferring the function(s) of a disordered protein region remains a major challenge. Computational methods have proven particularly relevant for studying IDPs: on the sequence level their dependence on distinct characteristics determined by the local amino acid context makes sequence-based prediction algorithms viable and reliable tools for large scale analyses, while on the structure level the in silico integration of fundamentally different experimental data types is essential to describe the behavior of a flexible protein chain. Here, we offer an overview of the latest developments and computational techniques that aim to uncover how protein function is connected to intrinsic disorder. PMID:26301226
Computational approaches to understanding protein aggregation in neurodegeneration
Redler, Rachel L.; Shirvanyants, David; Dagliyan, Onur; Ding, Feng; Kim, Doo Nam; Kota, Pradeep; Proctor, Elizabeth A.; Ramachandran, Srinivas; Tandon, Arpit; Dokholyan, Nikolay V.
2014-01-01
The generation of toxic non-native protein conformers has emerged as a unifying thread among disorders such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Atomic-level detail regarding dynamical changes that facilitate protein aggregation, as well as the structural features of large-scale ordered aggregates and soluble non-native oligomers, would contribute significantly to current understanding of these complex phenomena and offer potential strategies for inhibiting formation of cytotoxic species. However, experimental limitations often preclude the acquisition of high-resolution structural and mechanistic information for aggregating systems. Computational methods, particularly those combine both all-atom and coarse-grained simulations to cover a wide range of time and length scales, have thus emerged as crucial tools for investigating protein aggregation. Here we review the current state of computational methodology for the study of protein self-assembly, with a focus on the application of these methods toward understanding of protein aggregates in human neurodegenerative disorders. PMID:24620031
A uniform approach for programming distributed heterogeneous computing systems
Grasso, Ivan; Pellegrini, Simone; Cosenza, Biagio; Fahringer, Thomas
2014-01-01
Large-scale compute clusters of heterogeneous nodes equipped with multi-core CPUs and GPUs are getting increasingly popular in the scientific community. However, such systems require a combination of different programming paradigms making application development very challenging. In this article we introduce libWater, a library-based extension of the OpenCL programming model that simplifies the development of heterogeneous distributed applications. libWater consists of a simple interface, which is a transparent abstraction of the underlying distributed architecture, offering advanced features such as inter-context and inter-node device synchronization. It provides a runtime system which tracks dependency information enforced by event synchronization to dynamically build a DAG of commands, on which we automatically apply two optimizations: collective communication pattern detection and device-host-device copy removal. We assess libWater’s performance in three compute clusters available from the Vienna Scientific Cluster, the Barcelona Supercomputing Center and the University of Innsbruck, demonstrating improved performance and scaling with different test applications and configurations. PMID:25844015
Inverse problems and computational cell metabolic models: a statistical approach
NASA Astrophysics Data System (ADS)
Calvetti, D.; Somersalo, E.
2008-07-01
In this article, we give an overview of the Bayesian modelling of metabolic systems at the cellular and subcellular level. The models are based on detailed description of key biochemical reactions occurring in tissue, which may in turn be compartmentalized into cytosol and mitochondria, and of transports between the compartments. The classical deterministic approach which models metabolic systems as dynamical systems with Michaelis-Menten kinetics, is replaced by a stochastic extension where the model parameters are interpreted as random variables with an appropriate probability density. The inverse problem of cell metabolism in this setting consists of estimating the density of the model parameters. After discussing some possible approaches to solving the problem, we address the issue of how to assess the reliability of the predictions of a stochastic model by proposing an output analysis in terms of model uncertainties. Visualization modalities for organizing the large amount of information provided by the Bayesian dynamic sensitivity analysis are also illustrated.
Jung, Hee-Jung; Purvine, Samuel O.; Kim, Hokeun; Petyuk, Vladislav A.; Hyung, Seok-Won; Monroe, Matthew E.; Mun, Dong-Gi; Kim, Kyong-Chul; Park, Jong-Moon; Kim, Su-Jin; Tolic, Nikola; Slysz, Gordon W.; Moore, Ronald J.; Zhao, Rui; Adkins, Joshua N.; Anderson, Gordon A.; Lee, Hookeun; Camp, David G.; Yu, Myeong-Hee; Smith, Richard D.; Lee, Sang-Won
2010-10-15
Accurate assignment of monoisotopic precursor masses to tandem mass spectrometric (MS/MS) data is a fundamental and critically important step for successful peptide identifications in mass spectrometry based proteomics. Here we describe an integrated approach that combines three previously reported methods of treating MS/MS data for precursor mass refinement. This combined method, “integrated Post-Experiment Monoisotopic Mass Refinement” (iPE MMR), integrates steps: 1) generation of refined MS/MS data by DeconMSn, 2) additional refinement of the resultant MS/MS data by a modified version of PE-MMR, and 3) elimination of systematic errors of precursor masses using DtaRefinery. iPE-MMR is the first method that utilizes all MS information from multiple MS scans of a precursor ion and multiple charge states of it in an MS scan to determine precursor mass. By combining the synergistic features of each of method, iPE MMR increases sensitivity in peptide identification and provides increased accuracy when applied to complex high-throughput proteomics data. iPE MMR also allows incorporating additional data processing step(s) or skipping step(s), if necessary, to enable new developments or applications of the tools, as each step of iPE MMR produces output data in a common and conventional format used in proteomics data processing.
ERIC Educational Resources Information Center
Honsberger, Marion M.
This project was conducted at Edmonds Community College to develop curriculum and materials for use in teaching hands-on, computer-assisted court reporting. The final product of the project was a course with support materials designed to teach court reporting students performance skills by which each can rapidly create perfect computer-aided…
A dynamical-systems approach for computing ice-affected streamflow
Holtschlag, David J.
1996-01-01
A dynamical-systems approach was developed and evaluated for computing ice-affected streamflow. The approach provides for dynamic simulation and parameter estimation of site-specific equations relating ice effects to routinely measured environmental variables. Comparison indicates that results from the dynamical-systems approach ranked higher than results from 11 analytical methods previously investigated on the basis of accuracy and feasibility criteria. Additional research will likely lead to further improvements in the approach.
Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach
Eslami-Mossallam, Behrouz; Schram, Raoul D.; Tompitak, Marco; van Noort, John; Schiessel, Helmut
2016-01-01
Eukaryotic DNA is strongly bent inside fundamental packaging units: the nucleosomes. It is known that their positions are strongly influenced by the mechanical properties of the underlying DNA sequence. Here we discuss the possibility that these mechanical properties and the concomitant nucleosome positions are not just a side product of the given DNA sequence, e.g. that of the genes, but that a mechanical evolution of DNA molecules might have taken place. We first demonstrate the possibility of multiplexing classical and mechanical genetic information using a computational nucleosome model. In a second step we give evidence for genome-wide multiplexing in Saccharomyces cerevisiae and Schizosacharomyces pombe. This suggests that the exact positions of nucleosomes play crucial roles in chromatin function. PMID:27272176
A computational approach to the twin paradox in curved spacetime
NASA Astrophysics Data System (ADS)
Fung, Kenneth K. H.; Clark, Hamish A.; Lewis, Geraint F.; Wu, Xiaofeng
2016-09-01
Despite being a major component in the teaching of special relativity, the twin ‘paradox’ is generally not examined in courses on general relativity. Due to the complexity of analytical solutions to the problem, the paradox is often neglected entirely, and students are left with an incomplete understanding of the relativistic behaviour of time. This article outlines a project, undertaken by undergraduate physics students at the University of Sydney, in which a novel computational method was derived in order to predict the time experienced by a twin following a number of paths between two given spacetime coordinates. By utilising this method, it is possible to make clear to students that following a geodesic in curved spacetime does not always result in the greatest experienced proper time.
Computational biology approach to uncover hepatitis C virus helicase operation.
Flechsig, Holger
2014-04-01
Hepatitis C virus (HCV) helicase is a molecular motor that splits nucleic acid duplex structures during viral replication, therefore representing a promising target for antiviral treatment. Hence, a detailed understanding of the mechanism by which it operates would facilitate the development of efficient drug-assisted therapies aiming to inhibit helicase activity. Despite extensive investigations performed in the past, a thorough understanding of the activity of this important protein was lacking since the underlying internal conformational motions could not be resolved. Here we review investigations that have been previously performed by us for HCV helicase. Using methods of structure-based computational modelling it became possible to follow entire operation cycles of this motor protein in structurally resolved simulations and uncover the mechanism by which it moves along the nucleic acid and accomplishes strand separation. We also discuss observations from that study in the light of recent experimental studies that confirm our findings.
Embodied cognition of movement decisions: a computational modeling approach.
Johnson, Joseph G
2009-01-01
This chapter presents a cognitive computational view of decision making as the search for, and accumulation of, evidence for options under consideration. It is based on existing models that have been successful in traditional decision tasks involving preferential choice. The model assumes shifting attention over time that determines momentary inputs to an evolving preference state. In this chapter, the cognitive model is extended to illustrate how links from the motor system may be incorporated. These links can basically be categorized into one of three influences: modifying the subjective evaluation of choice options, restricting attention, and altering the options that are to be found in the choice set. The implications for the formal model are introduced and preliminary evidence is drawn from the extant literature.
Open-ended approaches to science assessment using computers
NASA Astrophysics Data System (ADS)
Singley, Mark K.; Taft, Hessy L.
1995-03-01
We discuss the potential role of technology in evaluating learning outcomes in large-scale, widespread science assessments of the kind typically done at ETS, such as the GRE, or the College Board SAT II Subject Tests. We describe the current state-of-the-art in this area, as well as briefly outline the history of technology in large-scale science assessment and ponder possibilities for the future. We present examples from our own work in the domain of chemistry, in which we are designing problem solving interfaces and scoring programs for stoichiometric and other kinds of quantitative problem solving. We also present a new scientific reasoning item type that we are prototyping on the computer. It is our view that the technological infrastructure for large-scale constructed response science assessment is well on its way to being available, although many technical and practical hurdles remain.
Computational biology approach to uncover hepatitis C virus helicase operation
Flechsig, Holger
2014-01-01
Hepatitis C virus (HCV) helicase is a molecular motor that splits nucleic acid duplex structures during viral replication, therefore representing a promising target for antiviral treatment. Hence, a detailed understanding of the mechanism by which it operates would facilitate the development of efficient drug-assisted therapies aiming to inhibit helicase activity. Despite extensive investigations performed in the past, a thorough understanding of the activity of this important protein was lacking since the underlying internal conformational motions could not be resolved. Here we review investigations that have been previously performed by us for HCV helicase. Using methods of structure-based computational modelling it became possible to follow entire operation cycles of this motor protein in structurally resolved simulations and uncover the mechanism by which it moves along the nucleic acid and accomplishes strand separation. We also discuss observations from that study in the light of recent experimental studies that confirm our findings. PMID:24707123
Photonic reservoir computing: a new approach to optical information processing
NASA Astrophysics Data System (ADS)
Vandoorne, Kristof; Fiers, Martin; Verstraeten, David; Schrauwen, Benjamin; Dambre, Joni; Bienstman, Peter
2010-06-01
Despite ever increasing computational power, recognition and classification problems remain challenging to solve. Recently, advances have been made by the introduction of the new concept of reservoir computing. This is a methodology coming from the field of machine learning and neural networks that has been successfully used in several pattern classification problems, like speech and image recognition. Thus far, most implementations have been in software, limiting their speed and power efficiency. Photonics could be an excellent platform for a hardware implementation of this concept because of its inherent parallelism and unique nonlinear behaviour. Moreover, a photonic implementation offers the promise of massively parallel information processing with low power and high speed. We propose using a network of coupled Semiconductor Optical Amplifiers (SOA) and show in simulation that it could be used as a reservoir by comparing it to conventional software implementations using a benchmark speech recognition task. In spite of the differences with classical reservoir models, the performance of our photonic reservoir is comparable to that of conventional implementations and sometimes slightly better. As our implementation uses coherent light for information processing, we find that phase tuning is crucial to obtain high performance. In parallel we investigate the use of a network of photonic crystal cavities. The coupled mode theory (CMT) is used to investigate these resonators. A new framework is designed to model networks of resonators and SOAs. The same network topologies are used, but feedback is added to control the internal dynamics of the system. By adjusting the readout weights of the network in a controlled manner, we can generate arbitrary periodic patterns.
Nicholson, Anita; Tobin, Mary
2006-01-01
This presentation will discuss coupling commercial and customized computer-supported teaching aids to provide BSN nursing students with a friendly customer-centered self-study approach to psychomotor skill acquisition.
Chacón, Enrique; Tarazona, Pedro; Bresme, Fernando
2015-07-21
We present a new computational approach to quantify the area per lipid and the area compressibility modulus of biological membranes. Our method relies on the analysis of the membrane fluctuations using our recently introduced coupled undulatory (CU) mode [Tarazona et al., J. Chem. Phys. 139, 094902 (2013)], which provides excellent estimates of the bending modulus of model membranes. Unlike the projected area, widely used in computer simulations of membranes, the CU area is thermodynamically consistent. This new area definition makes it possible to accurately estimate the area of the undulating bilayer, and the area per lipid, by excluding any contributions related to the phospholipid protrusions. We find that the area per phospholipid and the area compressibility modulus features a negligible dependence with system size, making possible their computation using truly small bilayers, involving a few hundred lipids. The area compressibility modulus obtained from the analysis of the CU area fluctuations is fully consistent with the Hooke’s law route. Unlike existing methods, our approach relies on a single simulation, and no a priori knowledge of the bending modulus is required. We illustrate our method by analyzing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers using the coarse grained MARTINI force-field. The area per lipid and area compressibility modulus obtained with our method and the MARTINI forcefield are consistent with previous studies of these bilayers.
NASA Astrophysics Data System (ADS)
Chacón, Enrique; Tarazona, Pedro; Bresme, Fernando
2015-07-01
We present a new computational approach to quantify the area per lipid and the area compressibility modulus of biological membranes. Our method relies on the analysis of the membrane fluctuations using our recently introduced coupled undulatory (CU) mode [Tarazona et al., J. Chem. Phys. 139, 094902 (2013)], which provides excellent estimates of the bending modulus of model membranes. Unlike the projected area, widely used in computer simulations of membranes, the CU area is thermodynamically consistent. This new area definition makes it possible to accurately estimate the area of the undulating bilayer, and the area per lipid, by excluding any contributions related to the phospholipid protrusions. We find that the area per phospholipid and the area compressibility modulus features a negligible dependence with system size, making possible their computation using truly small bilayers, involving a few hundred lipids. The area compressibility modulus obtained from the analysis of the CU area fluctuations is fully consistent with the Hooke's law route. Unlike existing methods, our approach relies on a single simulation, and no a priori knowledge of the bending modulus is required. We illustrate our method by analyzing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers using the coarse grained MARTINI force-field. The area per lipid and area compressibility modulus obtained with our method and the MARTINI forcefield are consistent with previous studies of these bilayers.
Computational s-block thermochemistry with the correlation consistent composite approach.
DeYonker, Nathan J; Ho, Dustin S; Wilson, Angela K; Cundari, Thomas R
2007-10-25
The correlation consistent composite approach (ccCA) is a model chemistry that has been shown to accurately compute gas-phase enthalpies of formation for alkali and alkaline earth metal oxides and hydroxides (Ho, D. S.; DeYonker, N. J.; Wilson, A. K.; Cundari, T. R. J. Phys. Chem. A 2006, 110, 9767). The ccCA results contrast to more widely used model chemistries where calculated enthalpies of formation for such species can be in error by up to 90 kcal mol-1. In this study, we have applied ccCA to a more general set of 42 s-block molecules and compared the ccCA DeltaHf values to values obtained using the G3 and G3B model chemistries. Included in this training set are water complexes such as Na(H2O)n+ where n = 1 - 4, dimers and trimers of ionic compounds such as (LiCl)2 and (LiCl)3, and the largest ccCA computation to date: Be(acac)2, BeC10H14O4. Problems with the G3 model chemistries seem to be isolated to metal-oxygen bonded systems and Be-containing systems, as G3 and G3B still perform quite well with a 2.7 and 2.6 kcal mol-1 mean absolute deviation (MAD), respectively, for gas-phase enthalpies of formation. The MAD of the ccCA is only 2.2 kcal mol-1 for enthalpies of formation (DeltaHf) for all compounds studied herein. While this MAD is roughly double that found for a ccCA study of >350 main group (i.e., p-block) compounds, it is commensurate with typical experimental uncertainties for s-block complexes. Some molecules where G3/G3B and ccCA computed DeltaHf values deviate significantly from experiment, such as (LiCl)3, NaCN, and MgF, are inviting candidates for new experimental and high-level theoretical studies. PMID:17914764
Perturbation approach for nuclear magnetic resonance solid-state quantum computation
Berman, G. P.; Kamenev, D. I.; Tsifrinovich, V. I.
2003-01-01
A dynmore » amics of a nuclear-spin quantum computer with a large number ( L = 1000 ) of qubits is considered using a perturbation approach. Small parameters are introduced and used to compute the error in an implementation of an entanglement between remote qubits, using a sequence of radio-frequency pulses. The error is computed up to the different orders of the perturbation theory and tested using exact numerical solution.« less
Strategic Cognitive Sequencing: A Computational Cognitive Neuroscience Approach
Herd, Seth A.; Krueger, Kai A.; Kriete, Trenton E.; Huang, Tsung-Ren; Hazy, Thomas E.; O'Reilly, Randall C.
2013-01-01
We address strategic cognitive sequencing, the “outer loop” of human cognition: how the brain decides what cognitive process to apply at a given moment to solve complex, multistep cognitive tasks. We argue that this topic has been neglected relative to its importance for systematic reasons but that recent work on how individual brain systems accomplish their computations has set the stage for productively addressing how brain regions coordinate over time to accomplish our most impressive thinking. We present four preliminary neural network models. The first addresses how the prefrontal cortex (PFC) and basal ganglia (BG) cooperate to perform trial-and-error learning of short sequences; the next, how several areas of PFC learn to make predictions of likely reward, and how this contributes to the BG making decisions at the level of strategies. The third models address how PFC, BG, parietal cortex, and hippocampus can work together to memorize sequences of cognitive actions from instruction (or “self-instruction”). The last shows how a constraint satisfaction process can find useful plans. The PFC maintains current and goal states and associates from both of these to find a “bridging” state, an abstract plan. We discuss how these processes could work together to produce strategic cognitive sequencing and discuss future directions in this area. PMID:23935605
Computer-aided liver surgery planning: an augmented reality approach
NASA Astrophysics Data System (ADS)
Bornik, Alexander; Beichel, Reinhard; Reitinger, Bernhard; Gotschuli, Georg; Sorantin, Erich; Leberl, Franz W.; Sonka, Milan
2003-05-01
Surgical resection of liver tumors requires a detailed three-dimensional understanding of a complex arrangement of vasculature, liver segments and tumors inside the liver. In most cases, surgeons need to develop this understanding by looking at sequences of axial images from modalities like X-ray computed tomography. A system for liver surgery planning is reported that enables physicians to visualize and refine segmented input liver data sets, as well as to simulate and evaluate different resections plans. The system supports surgeons in finding the optimal treatment strategy for each patient and eases the data preparation process. The use of augmented reality contributes to a user-friendly design and simplifies complex interaction with 3D objects. The main function blocks developed so far are: basic augmented reality environment, user interface, rendering, surface reconstruction from segmented volume data sets, surface manipulation and quantitative measurement toolkit. The flexible design allows to add functionality via plug-ins. First practical evaluation steps have shown a good acceptance. Evaluation of the system is ongoing and future feedback from surgeons will be collected and used for design refinements.
Cai, C.; Rodet, T.; Mohammad-Djafari, A.; Legoupil, S.
2013-11-15
Purpose: Dual-energy computed tomography (DECT) makes it possible to get two fractions of basis materials without segmentation. One is the soft-tissue equivalent water fraction and the other is the hard-matter equivalent bone fraction. Practical DECT measurements are usually obtained with polychromatic x-ray beams. Existing reconstruction approaches based on linear forward models without counting the beam polychromaticity fail to estimate the correct decomposition fractions and result in beam-hardening artifacts (BHA). The existing BHA correction approaches either need to refer to calibration measurements or suffer from the noise amplification caused by the negative-log preprocessing and the ill-conditioned water and bone separation problem. To overcome these problems, statistical DECT reconstruction approaches based on nonlinear forward models counting the beam polychromaticity show great potential for giving accurate fraction images.Methods: This work proposes a full-spectral Bayesian reconstruction approach which allows the reconstruction of high quality fraction images from ordinary polychromatic measurements. This approach is based on a Gaussian noise model with unknown variance assigned directly to the projections without taking negative-log. Referring to Bayesian inferences, the decomposition fractions and observation variance are estimated by using the joint maximum a posteriori (MAP) estimation method. Subject to an adaptive prior model assigned to the variance, the joint estimation problem is then simplified into a single estimation problem. It transforms the joint MAP estimation problem into a minimization problem with a nonquadratic cost function. To solve it, the use of a monotone conjugate gradient algorithm with suboptimal descent steps is proposed.Results: The performance of the proposed approach is analyzed with both simulated and experimental data. The results show that the proposed Bayesian approach is robust to noise and materials. It is also
Expert systems - New approaches to computer-aided engineering
NASA Astrophysics Data System (ADS)
Dym, C. L.
This paper provides an overview of the burgeoning new field of expert (knowledge-based) systems. This survey is tutorial in nature, intended to convey the gestalt of such systems to engineers who are newly exposed to the field. The discussion includes definitions, basic concepts, expert system architecture, descriptions of some of the programming tools and environments with which knowledge-based systems can be built, and approaches to knowledge acquisition. Some currently extant expert systems are described en passant, including a few developed for engineering purposes. Comments follow on the engineering of knowledge, as both cultural and social processes. The paper closes with an assessment of the roles that expert systems can play in engineering analysis, design, planning, and education.
Diabetes of the brain: computational approaches and interventional strategies.
Narasimhan, Kothandaraman; Govindasamy, Meenakumari; Gauthaman, Kalamegam; Kamal, Mohammad A; Abuzenadeh, Adel M; Al-Qahtani, Mohammed; Kanagasabai, Rajaraman
2014-04-01
Diabetes mellitus (DM) is characterized by hyperglycemia either due to deficient insulin production (Type 1 Diabetes mellitus) or peripheral insulin resistance of the cells (Type 2 Diabetes mellitus). Both Type 1 Diabetes mellitus and Type 2 Diabetes mellitus are more prevalent and efforts are directed to actively control these metabolic syndromes. Currently, Alzheimer's disease (AD), is gaining popularity as 'Type 3 diabetes' or 'Diabetes of the brain' and it is now evident that this neurodegenerative disease has multiple shared pathology with DM. Alarming is the fact that the incidence of AD might double within the next two decades, and this is certain to cause devastating effects not only to the afflicted individual or the family, but also to the global economy. Methods to either delay the onset or inhibit the progression of AD are therefore necessary. Progressive dementia, increased deposition of amyloid- β protein, neurofibrillary tangles and neuritic plaques in the brain are some of the hallmarks of AD. More understanding of the disease at the cellular and molecular level will enable identifying the possible targets for intervention and pave way for either development of novel or modification of the existing therapeutic options. In this work we have performed semantic data mining analysis on a large collection of most recently published data and identified an updated list of common genes expressed in DM and AD. Functional analysis of these genes revealed both existing and missing links involved in a bigger network associated with both disease conditions. Thus we argue that computational analysis methods help not only in understanding the mechanistic links but also in narrowing down precise targets (genes, proteins, metabolites and signalling pathways) and provide the base for both disease intervention and development of therapeutic options.
A Computational Approach to Estimating Nondisjunction Frequency in Saccharomyces cerevisiae
Chu, Daniel B.; Burgess, Sean M.
2016-01-01
Errors segregating homologous chromosomes during meiosis result in aneuploid gametes and are the largest contributing factor to birth defects and spontaneous abortions in humans. Saccharomyces cerevisiae has long served as a model organism for studying the gene network supporting normal chromosome segregation. Measuring homolog nondisjunction frequencies is laborious, and involves dissecting thousands of tetrads to detect missegregation of individually marked chromosomes. Here we describe a computational method (TetFit) to estimate the relative contributions of meiosis I nondisjunction and random-spore death to spore inviability in wild type and mutant strains. These values are based on finding the best-fit distribution of 4, 3, 2, 1, and 0 viable-spore tetrads to an observed distribution. Using TetFit, we found that meiosis I nondisjunction is an intrinsic component of spore inviability in wild-type strains. We show proof-of-principle that the calculated average meiosis I nondisjunction frequency determined by TetFit closely matches empirically determined values in mutant strains. Using these published data sets, TetFit uncovered two classes of mutants: Class A mutants skew toward increased nondisjunction death, and include those with known defects in establishing pairing, recombination, and/or synapsis of homologous chromosomes. Class B mutants skew toward random spore death, and include those with defects in sister-chromatid cohesion and centromere function. Epistasis analysis using TetFit is facilitated by the low numbers of tetrads (as few as 200) required to compare the contributions to spore death in different mutant backgrounds. TetFit analysis does not require any special strain construction, and can be applied to previously observed tetrad distributions. PMID:26747203
A Computational Approach to Estimating Nondisjunction Frequency in Saccharomyces cerevisiae.
Chu, Daniel B; Burgess, Sean M
2016-03-01
Errors segregating homologous chromosomes during meiosis result in aneuploid gametes and are the largest contributing factor to birth defects and spontaneous abortions in humans. Saccharomyces cerevisiae has long served as a model organism for studying the gene network supporting normal chromosome segregation. Measuring homolog nondisjunction frequencies is laborious, and involves dissecting thousands of tetrads to detect missegregation of individually marked chromosomes. Here we describe a computational method (TetFit) to estimate the relative contributions of meiosis I nondisjunction and random-spore death to spore inviability in wild type and mutant strains. These values are based on finding the best-fit distribution of 4, 3, 2, 1, and 0 viable-spore tetrads to an observed distribution. Using TetFit, we found that meiosis I nondisjunction is an intrinsic component of spore inviability in wild-type strains. We show proof-of-principle that the calculated average meiosis I nondisjunction frequency determined by TetFit closely matches empirically determined values in mutant strains. Using these published data sets, TetFit uncovered two classes of mutants: Class A mutants skew toward increased nondisjunction death, and include those with known defects in establishing pairing, recombination, and/or synapsis of homologous chromosomes. Class B mutants skew toward random spore death, and include those with defects in sister-chromatid cohesion and centromere function. Epistasis analysis using TetFit is facilitated by the low numbers of tetrads (as few as 200) required to compare the contributions to spore death in different mutant backgrounds. TetFit analysis does not require any special strain construction, and can be applied to previously observed tetrad distributions. PMID:26747203
Moskon, Miha; Mraz, Miha
2014-01-01
We present several measures that can be used in de novo computational design of biological systems with information processing capabilities. Their main purpose is to objectively evaluate the behavior and identify the biological information processing structures with the best dynamical properties. They can be used to define constraints that allow one to simplify the design of more complex biological systems. These measures can be applied to existent computational design approaches in synthetic biology, i.e., rational and automatic design approaches. We demonstrate their use on a) the computational models of several basic information processing structures implemented with gene regulatory networks and b) on a modular design of a synchronous toggle switch.
Analyses of Physcomitrella patens Ankyrin Repeat Proteins by Computational Approach
Mahmood, Niaz; Tamanna, Nahid
2016-01-01
Ankyrin (ANK) repeat containing proteins are evolutionary conserved and have functions in crucial cellular processes like cell cycle regulation and signal transduction. In this study, through an entirely in silico approach using the first release of the moss genome annotation, we found that at least 54 ANK proteins are present in P. patens. Based on their differential domain composition, the identified ANK proteins were classified into nine subfamilies. Comparative analysis of the different subfamilies of ANK proteins revealed that P. patens contains almost all the known subgroups of ANK proteins found in the other angiosperm species except for the ones having the TPR domain. Phylogenetic analysis using full length protein sequences supported the subfamily classification where the members of the same subfamily almost always clustered together. Synonymous divergence (dS) and nonsynonymous divergence (dN) ratios showed positive selection for the ANK genes of P. patens which probably helped them to attain significant functional diversity during the course of evolution. Taken together, the data provided here can provide useful insights for future functional studies of the proteins from this superfamily as well as comparative studies of ANK proteins. PMID:27429806
Driving profile modeling and recognition based on soft computing approach.
Wahab, Abdul; Quek, Chai; Tan, Chin Keong; Takeda, Kazuya
2009-04-01
Advancements in biometrics-based authentication have led to its increasing prominence and are being incorporated into everyday tasks. Existing vehicle security systems rely only on alarms or smart card as forms of protection. A biometric driver recognition system utilizing driving behaviors is a highly novel and personalized approach and could be incorporated into existing vehicle security system to form a multimodal identification system and offer a greater degree of multilevel protection. In this paper, detailed studies have been conducted to model individual driving behavior in order to identify features that may be efficiently and effectively used to profile each driver. Feature extraction techniques based on Gaussian mixture models (GMMs) are proposed and implemented. Features extracted from the accelerator and brake pedal pressure were then used as inputs to a fuzzy neural network (FNN) system to ascertain the identity of the driver. Two fuzzy neural networks, namely, the evolving fuzzy neural network (EFuNN) and the adaptive network-based fuzzy inference system (ANFIS), are used to demonstrate the viability of the two proposed feature extraction techniques. The performances were compared against an artificial neural network (NN) implementation using the multilayer perceptron (MLP) network and a statistical method based on the GMM. Extensive testing was conducted and the results show great potential in the use of the FNN for real-time driver identification and verification. In addition, the profiling of driver behaviors has numerous other potential applications for use by law enforcement and companies dealing with buses and truck drivers. PMID:19258199
An integrative computational approach for prioritization of genomic variants
Dubchak, Inna; Balasubramanian, Sandhya; Wang, Sheng; Meydan, Cem; Sulakhe, Dinanath; Poliakov, Alexander; Börnigen, Daniela; Xie, Bingqing; Taylor, Andrew; Ma, Jianzhu; et al
2014-12-15
An essential step in the discovery of molecular mechanisms contributing to disease phenotypes and efficient experimental planning is the development of weighted hypotheses that estimate the functional effects of sequence variants discovered by high-throughput genomics. With the increasing specialization of the bioinformatics resources, creating analytical workflows that seamlessly integrate data and bioinformatics tools developed by multiple groups becomes inevitable. Here we present a case study of a use of the distributed analytical environment integrating four complementary specialized resources, namely the Lynx platform, VISTA RViewer, the Developmental Brain Disorders Database (DBDB), and the RaptorX server, for the identification of high-confidence candidatemore » genes contributing to pathogenesis of spina bifida. The analysis resulted in prediction and validation of deleterious mutations in the SLC19A placental transporter in mothers of the affected children that causes narrowing of the outlet channel and therefore leads to the reduced folate permeation rate. The described approach also enabled correct identification of several genes, previously shown to contribute to pathogenesis of spina bifida, and suggestion of additional genes for experimental validations. The study demonstrates that the seamless integration of bioinformatics resources enables fast and efficient prioritization and characterization of genomic factors and molecular networks contributing to the phenotypes of interest.« less
An integrative computational approach for prioritization of genomic variants
Dubchak, Inna; Balasubramanian, Sandhya; Wang, Sheng; Meydan, Cem; Sulakhe, Dinanath; Poliakov, Alexander; Börnigen, Daniela; Xie, Bingqing; Taylor, Andrew; Ma, Jianzhu; Paciorkowski, Alex R.; Mirzaa, Ghayda M.; Dave, Paul; Agam, Gady; Xu, Jinbo; Al-Gazali, Lihadh; Mason, Christopher E.; Ross, M. Elizabeth; Maltsev, Natalia; Gilliam, T. Conrad; Huang, Qingyang
2014-12-15
An essential step in the discovery of molecular mechanisms contributing to disease phenotypes and efficient experimental planning is the development of weighted hypotheses that estimate the functional effects of sequence variants discovered by high-throughput genomics. With the increasing specialization of the bioinformatics resources, creating analytical workflows that seamlessly integrate data and bioinformatics tools developed by multiple groups becomes inevitable. Here we present a case study of a use of the distributed analytical environment integrating four complementary specialized resources, namely the Lynx platform, VISTA RViewer, the Developmental Brain Disorders Database (DBDB), and the RaptorX server, for the identification of high-confidence candidate genes contributing to pathogenesis of spina bifida. The analysis resulted in prediction and validation of deleterious mutations in the SLC19A placental transporter in mothers of the affected children that causes narrowing of the outlet channel and therefore leads to the reduced folate permeation rate. The described approach also enabled correct identification of several genes, previously shown to contribute to pathogenesis of spina bifida, and suggestion of additional genes for experimental validations. The study demonstrates that the seamless integration of bioinformatics resources enables fast and efficient prioritization and characterization of genomic factors and molecular networks contributing to the phenotypes of interest.
An integrative computational approach for prioritization of genomic variants.
Dubchak, Inna; Balasubramanian, Sandhya; Wang, Sheng; Cem, Meydan; Meyden, Cem; Sulakhe, Dinanath; Poliakov, Alexander; Börnigen, Daniela; Xie, Bingqing; Taylor, Andrew; Ma, Jianzhu; Paciorkowski, Alex R; Mirzaa, Ghayda M; Dave, Paul; Agam, Gady; Xu, Jinbo; Al-Gazali, Lihadh; Mason, Christopher E; Ross, M Elizabeth; Maltsev, Natalia; Gilliam, T Conrad
2014-01-01
An essential step in the discovery of molecular mechanisms contributing to disease phenotypes and efficient experimental planning is the development of weighted hypotheses that estimate the functional effects of sequence variants discovered by high-throughput genomics. With the increasing specialization of the bioinformatics resources, creating analytical workflows that seamlessly integrate data and bioinformatics tools developed by multiple groups becomes inevitable. Here we present a case study of a use of the distributed analytical environment integrating four complementary specialized resources, namely the Lynx platform, VISTA RViewer, the Developmental Brain Disorders Database (DBDB), and the RaptorX server, for the identification of high-confidence candidate genes contributing to pathogenesis of spina bifida. The analysis resulted in prediction and validation of deleterious mutations in the SLC19A placental transporter in mothers of the affected children that causes narrowing of the outlet channel and therefore leads to the reduced folate permeation rate. The described approach also enabled correct identification of several genes, previously shown to contribute to pathogenesis of spina bifida, and suggestion of additional genes for experimental validations. The study demonstrates that the seamless integration of bioinformatics resources enables fast and efficient prioritization and characterization of genomic factors and molecular networks contributing to the phenotypes of interest. PMID:25506935
An integrative computational approach for prioritization of genomic variants.
Dubchak, Inna; Balasubramanian, Sandhya; Wang, Sheng; Cem, Meydan; Meyden, Cem; Sulakhe, Dinanath; Poliakov, Alexander; Börnigen, Daniela; Xie, Bingqing; Taylor, Andrew; Ma, Jianzhu; Paciorkowski, Alex R; Mirzaa, Ghayda M; Dave, Paul; Agam, Gady; Xu, Jinbo; Al-Gazali, Lihadh; Mason, Christopher E; Ross, M Elizabeth; Maltsev, Natalia; Gilliam, T Conrad
2014-01-01
An essential step in the discovery of molecular mechanisms contributing to disease phenotypes and efficient experimental planning is the development of weighted hypotheses that estimate the functional effects of sequence variants discovered by high-throughput genomics. With the increasing specialization of the bioinformatics resources, creating analytical workflows that seamlessly integrate data and bioinformatics tools developed by multiple groups becomes inevitable. Here we present a case study of a use of the distributed analytical environment integrating four complementary specialized resources, namely the Lynx platform, VISTA RViewer, the Developmental Brain Disorders Database (DBDB), and the RaptorX server, for the identification of high-confidence candidate genes contributing to pathogenesis of spina bifida. The analysis resulted in prediction and validation of deleterious mutations in the SLC19A placental transporter in mothers of the affected children that causes narrowing of the outlet channel and therefore leads to the reduced folate permeation rate. The described approach also enabled correct identification of several genes, previously shown to contribute to pathogenesis of spina bifida, and suggestion of additional genes for experimental validations. The study demonstrates that the seamless integration of bioinformatics resources enables fast and efficient prioritization and characterization of genomic factors and molecular networks contributing to the phenotypes of interest.
Effects of artificial gravity on the cardiovascular system: Computational approach
NASA Astrophysics Data System (ADS)
Diaz Artiles, Ana; Heldt, Thomas; Young, Laurence R.
2016-09-01
steady-state cardiovascular behavior during sustained artificial gravity and exercise. Further validation of the model was performed using experimental data from the combined exercise and artificial gravity experiments conducted on the MIT CRC, and these results will be presented separately in future publications. This unique computational framework can be used to simulate a variety of centrifuge configuration and exercise intensities to improve understanding and inform decisions about future implementation of artificial gravity in space.
ERIC Educational Resources Information Center
de Vries, Hein; Brug, Johannes
1999-01-01
Introduces computerized tailoring and provides a brief overview of its elements and applications as well as of the papers of this issue. The articles describe the application of behavioral change theories to this new approach, advantages of computer-tailored intervention over more general mass media approaches, their effectiveness and future…
ERIC Educational Resources Information Center
Hwang, Gwo-Jen; Sung, Han-Yu; Hung, Chun-Ming; Yang, Li-Hsueh; Huang, Iwen
2013-01-01
Educational computer games have been recognized as being a promising approach for motivating students to learn. Nevertheless, previous studies have shown that without proper learning strategies or supportive models, the learning achievement of students might not be as good as expected. In this study, a knowledge engineering approach is proposed…
Computational model of precision grip in Parkinson's disease: a utility based approach.
Gupta, Ankur; Balasubramani, Pragathi P; Chakravarthy, V Srinivasa
2013-01-01
We propose a computational model of Precision Grip (PG) performance in normal subjects and Parkinson's Disease (PD) patients. Prior studies on grip force generation in PD patients show an increase in grip force during ON medication and an increase in the variability of the grip force during OFF medication (Ingvarsson et al., 1997; Fellows et al., 1998). Changes in grip force generation in dopamine-deficient PD conditions strongly suggest contribution of the Basal Ganglia, a deep brain system having a crucial role in translating dopamine signals to decision making. The present approach is to treat the problem of modeling grip force generation as a problem of action selection, which is one of the key functions of the Basal Ganglia. The model consists of two components: (1) the sensory-motor loop component, and (2) the Basal Ganglia component. The sensory-motor loop component converts a reference position and a reference grip force, into lift force and grip force profiles, respectively. These two forces cooperate in grip-lifting a load. The sensory-motor loop component also includes a plant model that represents the interaction between two fingers involved in PG, and the object to be lifted. The Basal Ganglia component is modeled using Reinforcement Learning with the significant difference that the action selection is performed using utility distribution instead of using purely Value-based distribution, thereby incorporating risk-based decision making. The proposed model is able to account for the PG results from normal and PD patients accurately (Ingvarsson et al., 1997; Fellows et al., 1998). To our knowledge the model is the first model of PG in PD conditions. PMID:24348373
Combined Experimental and Computational Approach to Predict the Glass-Water Reaction
Pierce, Eric M; Bacon, Diana
2011-01-01
The use of mineral and glass dissolution rates measured in laboratory experiments to predict the weathering of primary minerals and volcanic and nuclear waste glasses in field studies requires the construction of rate models that accurately describe the weathering process over geologic time-scales. Additionally, the need to model the long-term behavior of nuclear waste glass for the purpose of estimating radionuclide release rates requires that rate models are validated with long-term experiments. Several long-term test methods have been developed to accelerate the glass-water reaction [drip test, vapor hydration test, product consistency test-B, and pressurized unsaturated flow (PUF)], thereby reducing the duration required to evaluate long-term performance. Currently, the PUF test is the only method that mimics the unsaturated hydraulic properties expected in a subsurface disposal facility and simultaneously monitors the glass-water reaction. PUF tests are being conducted to accelerate the weathering of glass and validate the model parameters being used to predict long-term glass behavior. A one-dimensional reactive chemical transport simulation of glass dissolution and secondary phase formation during a 1.5-year long PUF experiment was conducted with the subsurface transport over reactive multi-phases code. Results show that parameterization of the computer model by combining direct bench-scale laboratory measurements and thermodynamic data provides an integrated approach to predicting glass behavior over the length of the experiment. Over the 1.5-year long test duration, the rate decreased from 0.2 to 0.01 g/(m2 d) base on B release. The observed decrease is approximately two orders of magnitude higher than the decrease observed under static conditions with the SON68 glass (estimated to be a decrease by 4 orders of magnitude) and suggest the gel-layer properties are less protective under these dynamic conditions.
Combined Experimental and Computational Approach to Predict the Glass-Water Reaction
Pierce, Eric M.; Bacon, Diana H.
2011-10-01
The use of mineral and glass dissolution rates measured in laboratory experiments to predict the weathering of primary minerals and volcanic and nuclear waste glasses in field studies requires the construction of rate models that accurately describe the weathering process over geologic timescales. Additionally, the need to model the long-term behavior of nuclear waste glass for the purpose of estimating radionuclide release rates requires that rate models be validated with long-term experiments. Several long-term test methods have been developed to accelerate the glass-water reaction [drip test, vapor hydration test, product consistency test B, and pressurized unsaturated flow (PUF)], thereby reducing the duration required to evaluate long-term performance. Currently, the PUF test is the only method that mimics the unsaturated hydraulic properties expected in a subsurface disposal facility and simultaneously monitors the glass-water reaction. PUF tests are being conducted to accelerate the weathering of glass and validate the model parameters being used to predict long-term glass behavior. A one-dimensional reactive chemical transport simulation of glass dissolution and secondary phase formation during a 1.5-year-long PUF experiment was conducted with the Subsurface Transport Over Reactive Multiphases (STORM) code. Results show that parameterization of the computer model by combining direct bench scale laboratory measurements and thermodynamic data provides an integrated approach to predicting glass behavior over the length of the experiment. Over the 1.5-year-long test duration, the rate decreased from 0.2 to 0.01 g/(m2 day) based on B release for low-activity waste glass LAWA44. The observed decrease is approximately two orders of magnitude higher than the decrease observed under static conditions with the SON68 glass (estimated to be a decrease by four orders of magnitude) and suggests that the gel-layer properties are less protective under these dynamic
NASA Astrophysics Data System (ADS)
Li, Haiyan; Huang, Yunbao; Jiang, Shaoen; Jing, Longfei; Ding, Yongkun
2015-08-01
Radiation flux computation on the target is very important for laser driven Inertial Confinement Fusion, and view-factor based equation models (MacFarlane, 2003; Srivastava et al., 2000) are often used to compute this radiation flux on the capsule or samples inside the hohlraum. However, the equation models do not lead to sparse matrices and may involve an intensive solution process when discrete mesh elements become smaller and the number of equations increases. An efficient approach for the computation of radiation flux is proposed in this paper, in which, (1) symmetric and positive definite properties are achieved by transformation, and (2) an efficient Cholesky factorization algorithm is applied to significantly accelerate such equations models solving process. Finally, two targets on a laser facility built in China are considered to validate the computing efficiency of present approach. The results show that the radiation flux computation can be accelerated by a factor of 2.
A new computer approach to mixed feature classification for forestry application
NASA Technical Reports Server (NTRS)
Kan, E. P.
1976-01-01
A computer approach for mapping mixed forest features (i.e., types, classes) from computer classification maps is discussed. Mixed features such as mixed softwood/hardwood stands are treated as admixtures of softwood and hardwood areas. Large-area mixed features are identified and small-area features neglected when the nominal size of a mixed feature can be specified. The computer program merges small isolated areas into surrounding areas by the iterative manipulation of the postprocessing algorithm that eliminates small connected sets. For a forestry application, computer-classified LANDSAT multispectral scanner data of the Sam Houston National Forest were used to demonstrate the proposed approach. The technique was successful in cleaning the salt-and-pepper appearance of multiclass classification maps and in mapping admixtures of softwood areas and hardwood areas. However, the computer-mapped mixed areas matched very poorly with the ground truth because of inadequate resolution and inappropriate definition of mixed features.
Fillippi, Anthony; Bhaduri, Budhendra L; Naughton, III, Thomas J; King, Amy L; Scott, Stephen L; Guneralp, Inci
2012-01-01
For aquatic studies, radiative transfer (RT) modeling can be used to compute hyperspectral above-surface remote sensing reflectance that can be utilized for inverse model development. Inverse models can provide bathymetry and inherent- and bottom-optical property estimation. Because measured oceanic field/organic datasets are often spatio-temporally sparse, synthetic data generation is useful in yielding sufficiently large datasets for inversion model development; however, these forward-modeled data are computationally expensive and time-consuming to generate. This study establishes the magnitude of wall-clock-time savings achieved for performing large, aquatic RT batch-runs using parallel computing versus a sequential approach. Given 2,600 simulations and identical compute-node characteristics, sequential architecture required {approx}100 hours until termination, whereas a parallel approach required only {approx}2.5 hours (42 compute nodes) - a 40x speed-up. Tools developed for this parallel execution are discussed.
Filippi, Anthony M; Bhaduri, Budhendra L; Naughton, III, Thomas J; King, Amy L; Scott, Stephen L; Guneralp, Inci
2012-01-01
Abstract For aquatic studies, radiative transfer (RT) modeling can be used to compute hyperspectral above-surface remote sensing reflectance that can be utilized for inverse model development. Inverse models can provide bathymetry and inherent-and bottom-optical property estimation. Because measured oceanic field/organic datasets are often spatio-temporally sparse, synthetic data generation is useful in yielding sufficiently large datasets for inversion model development; however, these forward-modeled data are computationally expensive and time-consuming to generate. This study establishes the magnitude of wall-clock-time savings achieved for performing large, aquatic RT batch-runs using parallel computing versus a sequential approach. Given 2,600 simulations and identical compute-node characteristics, sequential architecture required ~100 hours until termination, whereas a parallel approach required only ~2.5 hours (42 compute nodes) a 40x speed-up. Tools developed for this parallel execution are discussed.
Friedrich, Jan O; Beyene, Joseph; Adhikari, Neill KJ
2009-01-01
statistically significant. Conclusion We have shown that alternative reasonable methodological approaches to the rosiglitazone meta-analysis can yield increased or decreased risks that are either statistically significant or not significant at the p = 0.05 level for both myocardial infarction and cardiovascular death. Completion of ongoing trials may help to generate more accurate estimates of rosiglitazone's effect on cardiovascular outcomes. However, given that almost all point estimates suggest harm rather than benefit and the availability of alternative agents, the use of rosiglitazone may greatly decline prior to more definitive safety data being generated. PMID:19134216
Hybrid approach for fast occlusion processing in computer-generated hologram calculation.
Gilles, Antonin; Gioia, Patrick; Cozot, Rémi; Morin, Luce
2016-07-10
A hybrid approach for fast occlusion processing in computer-generated hologram calculation is studied in this paper. The proposed method is based on the combination of two commonly used approaches that complement one another: the point-source and wave-field approaches. By using these two approaches together, the proposed method thus takes advantage of both of them. In this method, the 3D scene is first sliced into several depth layers parallel to the hologram plane. Light scattered by the scene is then propagated and shielded from one layer to another using either a point-source or a wave-field approach according to a threshold criterion on the number of points within the layer. Finally, the hologram is obtained by computing the propagation of light from the nearest layer to the hologram plane. Experimental results reveal that the proposed method does not produce any visible artifact and outperforms both the point-source and wave-field approaches.
NASA Astrophysics Data System (ADS)
Igityan, Nune
2014-05-01
Land use and land cover (LULC) constitutes a key variable of the Earth's system that has in general shown a close correlation with human activities and the physical environment. Describing the pattern and the spatial distribution of LULC is traditionally based on remote sensing data analysis and, evidently, one of the most commonly techniques applied has been image classification. The main objective of the present study has been to evaluate the combined use of Hyperion hyperspectral imagery with a range of supervised classification algorithms widely available today for discriminating LULC classes in a typical Mediterranean setting. Accuracy assessment of the derived thematic maps was based on the analysis of the classification confusion matrix statistics computed for each classification map, using for consistency the same set of validation points. Those were selected on the basis of photo-interpretation of high resolution aerial imagery and of panchromatic imagery available for the studied region at the time of the Hyperion overpass. Results indicated close classification accuracy between the different classifiers with the SVMs outperforming the other classification approaches. The higher classification accuracy by SVMs was attributed principally to the ability of this classifier to identify an optimal separating hyperplane for classes' separation which allows a low generalisation error, thus producing the best possible classes' separation. Although all classifiers produced close results, SVMs generally appeared most useful in describing the spatial distribution and the cover density of each land cover category. All in all, this study demonstrated that, provided that a Hyperion hyperspectral imagery can be made available at regular time intervals over a given region, when combined with SVMs classifiers, can potentially enable a wider approach in land use/cover mapping. This can be of particular importance, especially for regions like in the Mediterranean basin
Computational Approach for Ranking Mutant Enzymes According to Catalytic Reaction Rates
Kumarasiri, Malika; Baker, Gregory A.; Soudackov, Alexander V.
2009-01-01
A computationally efficient approach for ranking mutant enzymes according to the catalytic reaction rates is presented. This procedure requires the generation and equilibration of the mutant structures, followed by the calculation of partial free energy curves using an empirical valence bond potential in conjunction with biased molecular dynamics simulations and umbrella integration. The individual steps are automated and optimized for computational efficiency. This approach is used to rank a series of 15 dihydrofolate reductase mutants according to the hydride transfer reaction rate. The agreement between the calculated and experimental changes in the free energy barrier upon mutation is encouraging. The computational approach predicts the correct direction of the change in free energy barrier for all mutants, and the correlation coefficient between the calculated and experimental data is 0.82. This general approach for ranking protein designs has implications for protein engineering and drug design. PMID:19235997
NASA Astrophysics Data System (ADS)
Zhang, Yong; Zhang, Kun; Pang, Jinglong
2016-01-01
This paper focuses on the study of topological features in teleportation-based quantum computation and aims at presenting a detailed review on teleportation-based quantum computation (Gottesman and Chuang in Nature 402: 390, 1999). In the extended Temperley-Lieb diagrammatical approach, we clearly show that such topological features bring about the fault-tolerant construction of both universal quantum gates and four-partite entangled states more intuitive and simpler. Furthermore, we describe the Yang-Baxter gate by its extended Temperley-Lieb configuration and then study teleportation-based quantum circuit models using the Yang-Baxter gate. Moreover, we discuss the relationship between the extended Temperley-Lieb diagrammatical approach and the Yang-Baxter gate approach. With these research results, we propose a worthwhile subject, the extended Temperley-Lieb diagrammatical approach, for physicists in quantum information and quantum computation.
NASA Astrophysics Data System (ADS)
Merced-Grafals, Emmanuelle J.; Dávila, Noraica; Ge, Ning; Williams, R. Stanley; Strachan, John Paul
2016-09-01
Beyond use as high density non-volatile memories, memristors have potential as synaptic components of neuromorphic systems. We investigated the suitability of tantalum oxide (TaOx) transistor-memristor (1T1R) arrays for such applications, particularly the ability to accurately, repeatedly, and rapidly reach arbitrary conductance states. Programming is performed by applying an adaptive pulsed algorithm that utilizes the transistor gate voltage to control the SET switching operation and increase programming speed of the 1T1R cells. We show the capability of programming 64 conductance levels with <0.5% average accuracy using 100 ns pulses and studied the trade-offs between programming speed and programming error. The algorithm is also utilized to program 16 conductance levels on a population of cells in the 1T1R array showing robustness to cell-to-cell variability. In general, the proposed algorithm results in approximately 10× improvement in programming speed over standard algorithms that do not use the transistor gate to control memristor switching. In addition, after only two programming pulses (an initialization pulse followed by a programming pulse), the resulting conductance values are within 12% of the target values in all cases. Finally, endurance of more than 106 cycles is shown through open-loop (single pulses) programming across multiple conductance levels using the optimized gate voltage of the transistor. These results are relevant for applications that require high speed, accurate, and repeatable programming of the cells such as in neural networks and analog data processing.
Computational approach to nuclear magnetic resonance in 1-Alkyl-3-methylimidazolium ionic liquids.
Palomar, Jose; Ferro, Victor R; Gilarranz, Miguel A; Rodriguez, Juan J
2007-01-11
A quantum-chemical computational approach to accurately predict the nuclear magnetic resonance (NMR) properties of 1-alkyl-3-methylimidazolium ionic liquids has been performed by the gauge-including atomic orbitals method at the B3LYP/6-31++G** level using different simulated ionic liquid environments. The first molecular model chosen to describe the ionic liquid system includes the gas-phase optimized structures of ion pairs and separated ions of a series of imidazolium salts containing methyl, butyl, and octyl substituents and PF6-, BF4-, and Br- anions. In addition, a continuum polarizable model of solvation has been applied to predict the effects of the medium polarity on the molecular properties of 1,3-dimethylimidazolium hexafluorophosphate (MmimPF6). Furthermore, the specific acidic and basic solute-solvent interactions have been simulated by a discrete solvation model based on molecular clusters formed by MmimPF6 species and a discrete number of water molecules. The computational prediction of the NMR spectra allows a consistent interpretation of the dispersed experimental evidence in the literature. The following are main contributions of this work: (a) Theoretical results state the presence of a chemical equilibrium between ion-pair aggregates and solvent-separated counterions of 1-alkyl-3-methylimidazolium salts which is tuned by the solvent environment; thus, strong specific (acidic and basic) and nonspecific (polarity and polarizability) solvent interactions are predicted favoring the dissociated ionic species. (b) The calculated 1H and 13C NMR properties of these ionic liquids are revealed as highly dependent on the nature of solute-solvent interactions. Thus, the chemical shift of the hydrogen atom in position two of the imidazolium ring is deviated to high values by the specific interactions with water molecules, whereas nonspecific interaction with water (as a solvent) affects, in the opposite direction, this 1H NMR parameter. (c) Last, current
Barone, Vincenzo; Bloino, Julien; Biczysko, Malgorzata; Santoro, Fabrizio
2009-03-10
A general and effective time-independent approach to compute vibrationally resolved electronic spectra from first principles has been integrated into the Gaussian computational chemistry package. This computational tool offers a simple and easy-to-use way to compute theoretical spectra starting from geometry optimization and frequency calculations for each electronic state. It is shown that in such a way it is straightforward to combine calculation of Franck-Condon integrals with any electronic computational model. The given examples illustrate the calculation of absorption and emission spectra, all in the UV-vis region, of various systems from small molecules to large ones, in gas as well as in condensed phases. The computational models applied range from fully quantum mechanical descriptions to discrete/continuum quantum mechanical/molecular mechanical/polarizable continuum models. PMID:26610221
Use of Integrated Computational Approaches in the Search for New Therapeutic Agents.
Persico, Marco; Di Dato, Antonio; Orteca, Nausicaa; Cimino, Paola; Novellino, Ettore; Fattorusso, Caterina
2016-09-01
Computer-aided drug discovery plays a strategic role in the development of new potential therapeutic agents. Nevertheless, the modeling of biological systems still represents a challenge for computational chemists and at present a single computational method able to face such challenge is not available. This prompted us, as computational medicinal chemists, to develop in-house methodologies by mixing various bioinformatics and computational tools. Importantly, thanks to multi-disciplinary collaborations, our computational studies were integrated and validated by experimental data in an iterative process. In this review, we describe some recent applications of such integrated approaches and how they were successfully applied in i) the search of new allosteric inhibitors of protein-protein interactions and ii) the development of new redox-active antimalarials from natural leads. PMID:27546035
Use of Integrated Computational Approaches in the Search for New Therapeutic Agents.
Persico, Marco; Di Dato, Antonio; Orteca, Nausicaa; Cimino, Paola; Novellino, Ettore; Fattorusso, Caterina
2016-09-01
Computer-aided drug discovery plays a strategic role in the development of new potential therapeutic agents. Nevertheless, the modeling of biological systems still represents a challenge for computational chemists and at present a single computational method able to face such challenge is not available. This prompted us, as computational medicinal chemists, to develop in-house methodologies by mixing various bioinformatics and computational tools. Importantly, thanks to multi-disciplinary collaborations, our computational studies were integrated and validated by experimental data in an iterative process. In this review, we describe some recent applications of such integrated approaches and how they were successfully applied in i) the search of new allosteric inhibitors of protein-protein interactions and ii) the development of new redox-active antimalarials from natural leads.
Accurate quantum chemical calculations
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.
1989-01-01
An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.
Merced-Grafals, Emmanuelle J; Dávila, Noraica; Ge, Ning; Williams, R Stanley; Strachan, John Paul
2016-09-01
Beyond use as high density non-volatile memories, memristors have potential as synaptic components of neuromorphic systems. We investigated the suitability of tantalum oxide (TaOx) transistor-memristor (1T1R) arrays for such applications, particularly the ability to accurately, repeatedly, and rapidly reach arbitrary conductance states. Programming is performed by applying an adaptive pulsed algorithm that utilizes the transistor gate voltage to control the SET switching operation and increase programming speed of the 1T1R cells. We show the capability of programming 64 conductance levels with <0.5% average accuracy using 100 ns pulses and studied the trade-offs between programming speed and programming error. The algorithm is also utilized to program 16 conductance levels on a population of cells in the 1T1R array showing robustness to cell-to-cell variability. In general, the proposed algorithm results in approximately 10× improvement in programming speed over standard algorithms that do not use the transistor gate to control memristor switching. In addition, after only two programming pulses (an initialization pulse followed by a programming pulse), the resulting conductance values are within 12% of the target values in all cases. Finally, endurance of more than 10(6) cycles is shown through open-loop (single pulses) programming across multiple conductance levels using the optimized gate voltage of the transistor. These results are relevant for applications that require high speed, accurate, and repeatable programming of the cells such as in neural networks and analog data processing.
Merced-Grafals, Emmanuelle J; Dávila, Noraica; Ge, Ning; Williams, R Stanley; Strachan, John Paul
2016-09-01
Beyond use as high density non-volatile memories, memristors have potential as synaptic components of neuromorphic systems. We investigated the suitability of tantalum oxide (TaOx) transistor-memristor (1T1R) arrays for such applications, particularly the ability to accurately, repeatedly, and rapidly reach arbitrary conductance states. Programming is performed by applying an adaptive pulsed algorithm that utilizes the transistor gate voltage to control the SET switching operation and increase programming speed of the 1T1R cells. We show the capability of programming 64 conductance levels with <0.5% average accuracy using 100 ns pulses and studied the trade-offs between programming speed and programming error. The algorithm is also utilized to program 16 conductance levels on a population of cells in the 1T1R array showing robustness to cell-to-cell variability. In general, the proposed algorithm results in approximately 10× improvement in programming speed over standard algorithms that do not use the transistor gate to control memristor switching. In addition, after only two programming pulses (an initialization pulse followed by a programming pulse), the resulting conductance values are within 12% of the target values in all cases. Finally, endurance of more than 10(6) cycles is shown through open-loop (single pulses) programming across multiple conductance levels using the optimized gate voltage of the transistor. These results are relevant for applications that require high speed, accurate, and repeatable programming of the cells such as in neural networks and analog data processing. PMID:27479054
A Combined Geometric Approach for Computational Fluid Dynamics on Dynamic Grids
NASA Technical Reports Server (NTRS)
Slater, John W.
1995-01-01
A combined geometric approach for computational fluid dynamics is presented for the analysis of unsteady flow about mechanisms in which its components are in moderate relative motion. For a CFD analysis, the total dynamics problem involves the dynamics of the aspects of geometry modeling, grid generation, and flow modeling. The interrelationships between these three aspects allow for a more natural formulation of the problem and the sharing of information which can be advantageous to the computation of the dynamics. The approach is applied to planar geometries with the use of an efficient multi-block, structured grid generation method to compute unsteady, two-dimensional and axisymmetric flow. The applications presented include the computation of the unsteady, inviscid flow about a hinged-flap with flap deflections and a high-speed inlet with centerbody motion as part of the unstart / restart operation.
Non-invasive computation of aortic pressure maps: a phantom-based study of two approaches
NASA Astrophysics Data System (ADS)
Delles, Michael; Schalck, Sebastian; Chassein, Yves; Müller, Tobias; Rengier, Fabian; Speidel, Stefanie; von Tengg-Kobligk, Hendrik; Kauczor, Hans-Ulrich; Dillmann, Rüdiger; Unterhinninghofen, Roland
2014-03-01
Patient-specific blood pressure values in the human aorta are an important parameter in the management of cardiovascular diseases. A direct measurement of these values is only possible by invasive catheterization at a limited number of measurement sites. To overcome these drawbacks, two non-invasive approaches of computing patient-specific relative aortic blood pressure maps throughout the entire aortic vessel volume are investigated by our group. The first approach uses computations from complete time-resolved, three-dimensional flow velocity fields acquired by phasecontrast magnetic resonance imaging (PC-MRI), whereas the second approach relies on computational fluid dynamics (CFD) simulations with ultrasound-based boundary conditions. A detailed evaluation of these computational methods under realistic conditions is necessary in order to investigate their overall robustness and accuracy as well as their sensitivity to certain algorithmic parameters. We present a comparative study of the two blood pressure computation methods in an experimental phantom setup, which mimics a simplified thoracic aorta. The comparative analysis includes the investigation of the impact of algorithmic parameters on the MRI-based blood pressure computation and the impact of extracting pressure maps in a voxel grid from the CFD simulations. Overall, a very good agreement between the results of the two computational approaches can be observed despite the fact that both methods used completely separate measurements as input data. Therefore, the comparative study of the presented work indicates that both non-invasive pressure computation methods show an excellent robustness and accuracy and can therefore be used for research purposes in the management of cardiovascular diseases.
A uniform algebraically-based approach to computational physics and efficient programming
NASA Astrophysics Data System (ADS)
Raynolds, James; Mullin, Lenore
2007-03-01
We present an approach to computational physics in which a common formalism is used both to express the physical problem as well as to describe the underlying details of how computation is realized on arbitrary multiprocessor/memory computer architectures. This formalism is the embodiment of a generalized algebra of multi-dimensional arrays (A Mathematics of Arrays) and an efficient computational implementation is obtained through the composition of of array indices (the psi-calculus) of algorithms defined using matrices, tensors, and arrays in general. The power of this approach arises from the fact that multiple computational steps (e.g. Fourier Transform followed by convolution, etc.) can be algebraically composed and reduced to an simplified expression (i.e. Operational Normal Form), that when directly translated into computer code, can be mathematically proven to be the most efficient implementation with the least number of temporary variables, etc. This approach will be illustrated in the context of a cache-optimized FFT that outperforms or is competitive with established library routines: ESSL, FFTW, IMSL, NAG.
A computational approach to detect and segment cytoplasm in muscle fiber images.
Guo, Yanen; Xu, Xiaoyin; Wang, Yuanyuan; Yang, Zhong; Wang, Yaming; Xia, Shunren
2015-06-01
We developed a computational approach to detect and segment cytoplasm in microscopic images of skeletal muscle fibers. The computational approach provides computer-aided analysis of cytoplasm objects in muscle fiber images to facilitate biomedical research. Cytoplasm in muscle fibers plays an important role in maintaining the functioning and health of muscular tissues. Therefore, cytoplasm is often used as a marker in broad applications of musculoskeletal research, including our search on treatment of muscular disorders such as Duchenne muscular dystrophy, a disease that has no available treatment. However, it is often challenging to analyze cytoplasm and quantify it given the large number of images typically generated in experiments and the large number of muscle fibers contained in each image. Manual analysis is not only time consuming but also prone to human errors. In this work we developed a computational approach to detect and segment the longitudinal sections of cytoplasm based on a modified graph cuts technique and iterative splitting method to extract cytoplasm objects from the background. First, cytoplasm objects are extracted from the background using the modified graph cuts technique which is designed to optimize an energy function. Second, an iterative splitting method is designed to separate the touching or adjacent cytoplasm objects from the results of graph cuts. We tested the computational approach on real data from in vitro experiments and found that it can achieve satisfactory performance in terms of precision and recall rates.
Mayorga, René V; Carrera, Jonathan
2007-06-01
This Paper presents an efficient approach for the fast computation of inverse continuous time variant functions with the proper use of Radial Basis Function Networks (RBFNs). The approach is based on implementing RBFNs for computing inverse continuous time variant functions via an overall damped least squares solution that includes a novel null space vector for singularities prevention. The singularities avoidance null space vector is derived from developing a sufficiency condition for singularities prevention that conduces to establish some characterizing matrices and an associated performance index.
An Approach to Integrate a Space-Time GIS Data Model with High Performance Computers
Wang, Dali; Zhao, Ziliang; Shaw, Shih-Lung
2011-01-01
In this paper, we describe an approach to integrate a Space-Time GIS data model on a high performance computing platform. The Space-Time GIS data model has been developed on a desktop computing environment. We use the Space-Time GIS data model to generate GIS module, which organizes a series of remote sensing data. We are in the process of porting the GIS module into an HPC environment, in which the GIS modules handle large dataset directly via parallel file system. Although it is an ongoing project, authors hope this effort can inspire further discussions on the integration of GIS on high performance computing platforms.
Anharmonic-potential-effective-charge approach for computing Raman cross sections of a gas
NASA Astrophysics Data System (ADS)
Kutteh, Ramzi; van Zandt, L. L.
1993-05-01
An anharmonic-potential-effective-charge approach for computing relative Raman intensities of a gas is developed. The equations of motion are set up and solved for the driven anharmonic molecular vibrations. An explicit expression for the differential polarizability tensor is derived and its properties discussed. This expression is then used within the context of Placzek's theory [Handbuch der Radiologie (Akademische Verlagsgesellschaft, Leipzig, 1934), Vol. VI] to compute the Raman cross section and depolarization ratio of a gas. The computation is carried out for the small molecules CO2, CS2, SO2, and CCl4; results are compared with experimental measurements and discussed.
Algorithmic approaches for computing elementary modes in large biochemical reaction networks.
Klamt, S; Gagneur, J; von Kamp, A
2005-12-01
The concept of elementary (flux) modes provides a rigorous description of pathways in metabolic networks and proved to be valuable in a number of applications. However, the computation of elementary modes is a hard computational task that gave rise to several variants of algorithms during the last years. This work brings substantial progresses to this issue. The authors start with a brief review of results obtained from previous work regarding (a) a unified framework for elementary-mode computation, (b) network compression and redundancy removal and (c) the binary approach by which elementary modes are determined as binary patterns reducing the memory demand drastically without loss of speed. Then the authors will address herein further issues. First, a new way to perform the elementarity tests required during the computation of elementary modes which empirically improves significantly the computation time in large networks is proposed. Second, a method to compute only those elementary modes where certain reactions are involved is derived. Relying on this method, a promising approach for computing EMs in a completely distributed manner by decomposing the full problem in arbitrarity many sub-tasks is presented. The new methods have been implemented in the freely available software tools FluxAnalyzer and Metatool and benchmark tests in realistic networks emphasise the potential of our proposed algorithms.
Federal Register 2010, 2011, 2012, 2013, 2014
2011-08-22
... Assumption Buster Workshop: ``Current Implementations of Cloud Computing Indicate a New Approach to Security... computing. The workshop on this topic will be held in Gaithersburg, MD on October 21, 2011. Assertion: ``Current implementations of cloud computing indicate a new approach to security'' Implementations of...
ERIC Educational Resources Information Center
Wang, Chu-Fu; Lin, Chih-Lung; Deng, Jien-Han
2012-01-01
Testing is an important stage of teaching as it can assist teachers in auditing students' learning results. A good test is able to accurately reflect the capability of a learner. Nowadays, Computer-Assisted Testing (CAT) is greatly improving traditional testing, since computers can automatically and quickly compose a proper test sheet to meet user…
Zhu, Shun; Travis, Sue M; Elcock, Adrian H
2013-07-01
A major current challenge for drug design efforts focused on protein kinases is the development of drug resistance caused by spontaneous mutations in the kinase catalytic domain. The ubiquity of this problem means that it would be advantageous to develop fast, effective computational methods that could be used to determine the effects of potential resistance-causing mutations before they arise in a clinical setting. With this long-term goal in mind, we have conducted a combined experimental and computational study of the thermodynamic effects of active-site mutations on a well-characterized and high-affinity interaction between a protein kinase and a small-molecule inhibitor. Specifically, we developed a fluorescence-based assay to measure the binding free energy of the small-molecule inhibitor, SB203580, to the p38α MAP kinase and used it measure the inhibitor's affinity for five different kinase mutants involving two residues (Val38 and Ala51) that contact the inhibitor in the crystal structure of the inhibitor-kinase complex. We then conducted long, explicit-solvent thermodynamic integration (TI) simulations in an attempt to reproduce the experimental relative binding affinities of the inhibitor for the five mutants; in total, a combined simulation time of 18.5 μs was obtained. Two widely used force fields - OPLS-AA/L and Amber ff99SB-ILDN - were tested in the TI simulations. Both force fields produced excellent agreement with experiment for three of the five mutants; simulations performed with the OPLS-AA/L force field, however, produced qualitatively incorrect results for the constructs that contained an A51V mutation. Interestingly, the discrepancies with the OPLS-AA/L force field could be rectified by the imposition of position restraints on the atoms of the protein backbone and the inhibitor without destroying the agreement for other mutations; the ability to reproduce experiment depended, however, upon the strength of the restraints' force constant
NASA Astrophysics Data System (ADS)
Fazanaro, Filipe I.; Soriano, Diogo C.; Suyama, Ricardo; Madrid, Marconi K.; Oliveira, José Raimundo de; Muñoz, Ignacio Bravo; Attux, Romis
2016-08-01
The characterization of nonlinear dynamical systems and their attractors in terms of invariant measures, basins of attractions and the structure of their vector fields usually outlines a task strongly related to the underlying computational cost. In this work, the practical aspects related to the use of parallel computing - specially the use of Graphics Processing Units (GPUS) and of the Compute Unified Device Architecture (CUDA) - are reviewed and discussed in the context of nonlinear dynamical systems characterization. In this work such characterization is performed by obtaining both local and global Lyapunov exponents for the classical forced Duffing oscillator. The local divergence measure was employed by the computation of the Lagrangian Coherent Structures (LCSS), revealing the general organization of the flow according to the obtained separatrices, while the global Lyapunov exponents were used to characterize the attractors obtained under one or more bifurcation parameters. These simulation sets also illustrate the required computation time and speedup gains provided by different parallel computing strategies, justifying the employment and the relevance of GPUS and CUDA in such extensive numerical approach. Finally, more than simply providing an overview supported by a representative set of simulations, this work also aims to be a unified introduction to the use of the mentioned parallel computing tools in the context of nonlinear dynamical systems, providing codes and examples to be executed in MATLAB and using the CUDA environment, something that is usually fragmented in different scientific communities and restricted to specialists on parallel computing strategies.
A dual-energy approach for improvement of the measurement consistency in computed tomography
NASA Astrophysics Data System (ADS)
Jansson, Anton; Pejryd, Lars
2016-11-01
Computed tomography is increasingly adopted by industries for metrological and material evaluation. The technology enables new measurement possibilities, while also challenging old measurement methods in their established territories. There are, however, uncertainties related with the computed tomography method. Investigation of multi-material components with, in particular, varying material thickness can result in unreliable measurements. In this paper the effects of multi-materials, and differing material thickness, on computed tomography measurement consistency has been studied. The aim of the study was to identify measurement inconsistencies and attempt to correct these with a dual-energy computed tomography approach. In this pursuit, a multi-material phantom was developed, containing reliable measurement points and custom-ability with regards to material combinations. A dual-energy method was developed and implemented using sequential acquisition and pre-reconstruction fusing of projections. It was found that measurements made on the multi-material phantom with a single computed tomography scan were highly inconsistent. It was also found that the dual-energy approach was able to reduce the measurement inconsistencies. However, more work is required with the automation of the dual-energy approach presented in this paper since it is highly operator dependant.
NASA Astrophysics Data System (ADS)
Carelli, Fabio; Gianturco, Francesco Antonio
2016-06-01
The interaction of low-energy scattering electrons/positrons with molecular targets characterized by a "supercritical" permanent dipole moment (≳2.0 D) presents special physical characteristics that affect their spatial distributions, around the nuclear network of the molecular partners, both above and below the energy thresholds. Such special states are described as either dipole scattering states (DSS) above thresholds or as dipole bound states (DBS) below thresholds. The details of their respective behaviour will be presented and discussed in this work in the case of the purinic DNA bases of adenine and guanine. The behavior of the additional electron, in particular, will be discussed in detail by providing new computational results that will be related to the findings from recent experiments on the same DNA bases, confirming the transient electron's behaviour surmised by them. This work is affectionately dedicated to Michael Allan on the occasion of his official retirement. We wish to this dear friend and outstanding scientist many years to come in the happy pursuit of his many scientific interests.Contribution to the Topical Issue "Advances in Positron and Electron Scattering", edited by Paulo Limao-Vieira, Gustavo Garcia, E. Krishnakumar, James Sullivan, Hajime Tanuma and Zoran Petrovic.
Learning Probabilities in Computer Engineering by Using a Competency- and Problem-Based Approach
ERIC Educational Resources Information Center
Khoumsi, Ahmed; Hadjou, Brahim
2005-01-01
Our department has redesigned its electrical and computer engineering programs by adopting a learning methodology based on competence development, problem solving, and the realization of design projects. In this article, we show how this pedagogical approach has been successfully used for learning probabilities and their application to computer…
An Overview of Three Approaches to Scoring Written Essays by Computer.
ERIC Educational Resources Information Center
Rudner, Lawrence; Gagne, Phill
2001-01-01
Describes the three most promising approaches to essay scoring by computer: (1) Project Essay Grade (PEG; E. Page, 1966); (2) Intelligent Essay Assessor (IEA; T. Landauer, 1997); and (3) E-rater (J. Burstein, Educational Testing Service). All of these proprietary systems return grades that correlate meaningfully with those of human raters. (SLD)
An Overview of Three Approaches to Scoring Written Essays by Computer. ERIC Digest.
ERIC Educational Resources Information Center
Rudner, Lawrence; Gagne, Phill
This digest describes the three most prominent approaches to essay scoring by computer: (1) Project Essay Grade (PEG), introduced by E. Page in 1966; (2) Intelligent Essay Assessor (IEA), introduced for essay grading in 1997 by T. Landauer and P. Foltz; and (3) e-rater, used by the Educational Testing Service and developed by J. Burstein. PEG…
Benson, W.H., R.T. Di Giulio, J.C. Cook, J. Freedman, R.L. Malek, C. Thompson and D. Versteeg. In press. Emerging Molecular and Computational Approaches for Cross-Species Extrapolations: A Workshop Summary Report (Abstract). To be presented at the SETAC Fourth World Congress, 14-...
A Computer-Based Spatial Learning Strategy Approach That Improves Reading Comprehension and Writing
ERIC Educational Resources Information Center
Ponce, Hector R.; Mayer, Richard E.; Lopez, Mario J.
2013-01-01
This article explores the effectiveness of a computer-based spatial learning strategy approach for improving reading comprehension and writing. In reading comprehension, students received scaffolded practice in translating passages into graphic organizers. In writing, students received scaffolded practice in planning to write by filling in graphic…
The Computational Experiment and Its Effects on Approach to Learning and Beliefs on Physics
ERIC Educational Resources Information Center
Psycharis, Sarantos
2011-01-01
Contemporary instructional approaches expect students to be active producers of knowledge. This leads to the need for creation of instructional tools and tasks that can offer students opportunities for active learning. This study examines the effect of a computational experiment as an instructional tool-for Grade 12 students, using a computer…
The Criterion-Related Validity of a Computer-Based Approach for Scoring Concept Maps
ERIC Educational Resources Information Center
Clariana, Roy B.; Koul, Ravinder; Salehi, Roya
2006-01-01
This investigation seeks to confirm a computer-based approach that can be used to score concept maps (Poindexter & Clariana, 2004) and then describes the concurrent criterion-related validity of these scores. Participants enrolled in two graduate courses (n=24) were asked to read about and research online the structure and function of the heart…
NASA Technical Reports Server (NTRS)
Bey, K. S.; Thornton, E. A.; Dechaumphai, P.; Ramakrishnan, R.
1985-01-01
Recent progress in the development of finite element methodology for the prediction of aerothermal loads is described. Two dimensional, inviscid computations are presented, but emphasis is placed on development of an approach extendable to three dimensional viscous flows. Research progress is described for: (1) utilization of a commerically available program to construct flow solution domains and display computational results, (2) development of an explicit Taylor-Galerkin solution algorithm, (3) closed form evaluation of finite element matrices, (4) vector computer programming strategies, and (5) validation of solutions. Two test problems of interest to NASA Langley aerothermal research are studied. Comparisons of finite element solutions for Mach 6 flow with other solution methods and experimental data validate fundamental capabilities of the approach for analyzing high speed inviscid compressible flows.
Using an Adjoint Approach to Eliminate Mesh Sensitivities in Computational Design
NASA Technical Reports Server (NTRS)
Nielsen, Eric J.; Park, Michael A.
2005-01-01
An algorithm for efficiently incorporating the effects of mesh sensitivities in a computational design framework is introduced. The method is based on an adjoint approach and eliminates the need for explicit linearizations of the mesh movement scheme with respect to the geometric parameterization variables, an expense that has hindered practical large-scale design optimization using discrete adjoint methods. The effects of the mesh sensitivities can be accounted for through the solution of an adjoint problem equivalent in cost to a single mesh movement computation, followed by an explicit matrix-vector product scaling with the number of design variables and the resolution of the parameterized surface grid. The accuracy of the implementation is established and dramatic computational savings obtained using the new approach are demonstrated using several test cases. Sample design optimizations are also shown.
Using an Adjoint Approach to Eliminate Mesh Sensitivities in Computational Design
NASA Technical Reports Server (NTRS)
Nielsen, Eric J.; Park, Michael A.
2006-01-01
An algorithm for efficiently incorporating the effects of mesh sensitivities in a computational design framework is introduced. The method is based on an adjoint approach and eliminates the need for explicit linearizations of the mesh movement scheme with respect to the geometric parameterization variables, an expense that has hindered practical large-scale design optimization using discrete adjoint methods. The effects of the mesh sensitivities can be accounted for through the solution of an adjoint problem equivalent in cost to a single mesh movement computation, followed by an explicit matrix-vector product scaling with the number of design variables and the resolution of the parameterized surface grid. The accuracy of the implementation is established and dramatic computational savings obtained using the new approach are demonstrated using several test cases. Sample design optimizations are also shown.
Redlarski, Grzegorz; Jaworski, Jacek
2013-10-01
This paper presents a new versatile approach to model severe human respiratory diseases via computer simulation. The proposed approach enables one to predict the time histories of various diseases via information accessible in medical publications. This knowledge is useful to bioengineers involved in the design and construction of medical devices that are employed for monitoring of respiratory condition. The approach provides the data that are crucial for testing diagnostic systems. This can be achieved without the necessity of probing the physiological details of the respiratory system as well as without identification of parameters that are based on measurement data.
Badran, Yasser Ali; Abdelaziz, Alsayed Saad; Shehab, Mohamed Ahmed; Mohamed, Hazem Abdelsabour Dief; Emara, Absel-Aziz Ali; Elnabtity, Ali Mohamed Ali; Ghanem, Maged Mohammed; ELHelaly, Hesham Abdel Azim
2016-01-01
Objective: The objective was to determine the predicting success of shock wave lithotripsy (SWL) using a combination of computed tomography based metric parameters to improve the treatment plan. Patients and Methods: Consecutive 180 patients with symptomatic upper urinary tract calculi 20 mm or less were enrolled in our study underwent extracorporeal SWL were divided into two main groups, according to the stone size, Group A (92 patients with stone ≤10 mm) and Group B (88 patients with stone >10 mm). Both groups were evaluated, according to the skin to stone distance (SSD) and Hounsfield units (≤500, 500–1000 and >1000 HU). Results: Both groups were comparable in baseline data and stone characteristics. About 92.3% of Group A rendered stone-free, whereas 77.2% were stone-free in Group B (P = 0.001). Furthermore, in both group SWL success rates was a significantly higher for stones with lower attenuation <830 HU than with stones >830 HU (P < 0.034). SSD were statistically differences in SWL outcome (P < 0.02). Simultaneous consideration of three parameters stone size, stone attenuation value, and SSD; we found that stone-free rate (SFR) was 100% for stone attenuation value <830 HU for stone <10 mm or >10 mm but total number SWL sessions and shock waves required for the larger stone group were higher than in the smaller group (P < 0.01). Furthermore, SFR was 83.3% and 37.5% for stone <10 mm, mean HU >830, SSD 90 mm and SSD >120 mm, respectively. On the other hand, SFR was 52.6% and 28.57% for stone >10 mm, mean HU >830, SSD <90 mm and SSD >120 mm, respectively. Conclusion: Stone size, stone density (HU), and SSD is simple to calculate and can be reported by radiologists to applying combined score help to augment predictive power of SWL, reduce cost, and improving of treatment strategies. PMID:27141192
Toward Accurate and Quantitative Comparative Metagenomics.
Nayfach, Stephen; Pollard, Katherine S
2016-08-25
Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341
Toward Accurate and Quantitative Comparative Metagenomics
Nayfach, Stephen; Pollard, Katherine S.
2016-01-01
Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341
NASA Technical Reports Server (NTRS)
Drake, Jeffrey T.; Prasad, Nadipuram R.
1999-01-01
This paper surveys recent advances in communications that utilize soft computing approaches to phase synchronization. Soft computing, as opposed to hard computing, is a collection of complementary methodologies that act in producing the most desirable control, decision, or estimation strategies. Recently, the communications area has explored the use of the principal constituents of soft computing, namely, fuzzy logic, neural networks, and genetic algorithms, for modeling, control, and most recently for the estimation of phase in phase-coherent communications. If the receiver in a digital communications system is phase-coherent, as is often the case, phase synchronization is required. Synchronization thus requires estimation and/or control at the receiver of an unknown or random phase offset.
A multiresolution approach to iterative reconstruction algorithms in X-ray computed tomography.
De Witte, Yoni; Vlassenbroeck, Jelle; Van Hoorebeke, Luc
2010-09-01
In computed tomography, the application of iterative reconstruction methods in practical situations is impeded by their high computational demands. Especially in high resolution X-ray computed tomography, where reconstruction volumes contain a high number of volume elements (several giga voxels), this computational burden prevents their actual breakthrough. Besides the large amount of calculations, iterative algorithms require the entire volume to be kept in memory during reconstruction, which quickly becomes cumbersome for large data sets. To overcome this obstacle, we present a novel multiresolution reconstruction, which greatly reduces the required amount of memory without significantly affecting the reconstructed image quality. It is shown that, combined with an efficient implementation on a graphical processing unit, the multiresolution approach enables the application of iterative algorithms in the reconstruction of large volumes at an acceptable speed using only limited resources. PMID:20350850
A concurrent hybrid Navier-Stokes/Euler approach to fluid dynamic computations
NASA Technical Reports Server (NTRS)
Tavella, Domingo A.; Djomehri, M. J.; Kislitzin, Katherine T.; Blake, Matthew W.; Erickson, Larry L.
1993-01-01
We present a methodology for the numerical simulation of flow fields by the simultaneous application of two distinct approaches to computational aerodynamics. We compute the three dimensional flow field of a missile at moderate angle of attack by dividing the flow field into two regions: a region near the surface where we use a structured grid and a Navier Stokes solver, and a region farther away from the surface where we utilize an unstructured grid and an Euler solver. The two solvers execute as independent UNIX processes either on the same machine or on two machines. The solvers communicate data across their common interfaces within the same machine or over the network. The computations indicate that extensively separated flow fields can be computed without significant distortion by combining viscous and inviscid solvers.
A computationally efficient approach for hidden-Markov model-augmented fingerprint-based positioning
NASA Astrophysics Data System (ADS)
Roth, John; Tummala, Murali; McEachen, John
2016-09-01
This paper presents a computationally efficient approach for mobile subscriber position estimation in wireless networks. A method of data scaling assisted by timing adjust is introduced in fingerprint-based location estimation under a framework which allows for minimising computational cost. The proposed method maintains a comparable level of accuracy to the traditional case where no data scaling is used and is evaluated in a simulated environment under varying channel conditions. The proposed scheme is studied when it is augmented by a hidden-Markov model to match the internal parameters to the channel conditions that present, thus minimising computational cost while maximising accuracy. Furthermore, the timing adjust quantity, available in modern wireless signalling messages, is shown to be able to further reduce computational cost and increase accuracy when available. The results may be seen as a significant step towards integrating advanced position-based modelling with power-sensitive mobile devices.
Arunyanak, Sirikarn P; Harris, Bryan T; Grant, Gerald T; Morton, Dean; Lin, Wei-Shao
2016-07-01
This report describes a digital approach for computer-guided surgery and immediate provisionalization in a partially edentulous patient. With diagnostic data obtained from cone-beam computed tomography and intraoral digital diagnostic scans, a digital pathway of virtual diagnostic waxing, a virtual prosthetically driven surgical plan, a computer-aided design and computer-aided manufacturing (CAD/CAM) surgical template, and implant-supported screw-retained interim restorations were realized with various open-architecture CAD/CAM systems. The optional CAD/CAM diagnostic casts with planned implant placement were also additively manufactured to facilitate preoperative inspection of the surgical template and customization of the CAD/CAM-fabricated interim restorations. PMID:26868961
Tangprasertchai, Narin S.; Zhang, Xiaojun; Ding, Yuan; Tham, Kenneth; Rohs, Remo; Haworth, Ian S.; Qin, Peter Z.
2015-01-01
The technique of site-directed spin labeling (SDSL) provides unique information on biomolecules by monitoring the behavior of a stable radical tag (i.e., spin label) using electron paramagnetic resonance (EPR) spectroscopy. In this chapter, we describe an approach in which SDSL is integrated with computational modeling to map conformations of nucleic acids. This approach builds upon a SDSL tool kit previously developed and validated, which includes three components: (i) a nucleotide-independent nitroxide probe, designated as R5, which can be efficiently attached at defined sites within arbitrary nucleic acid sequences; (ii) inter-R5 distances in the nanometer range, measured via pulsed EPR; and (iii) an efficient program, called NASNOX, that computes inter-R5 distances on given nucleic acid structures. Following a general framework of data mining, our approach uses multiple sets of measured inter-R5 distances to retrieve “correct” all-atom models from a large ensemble of models. The pool of models can be generated independently without relying on the inter-R5 distances, thus allowing a large degree of flexibility in integrating the SDSL-measured distances with a modeling approach best suited for the specific system under investigation. As such, the integrative experimental/computational approach described here represents a hybrid method for determining all-atom models based on experimentally-derived distance measurements. PMID:26477260
Tangprasertchai, Narin S; Zhang, Xiaojun; Ding, Yuan; Tham, Kenneth; Rohs, Remo; Haworth, Ian S; Qin, Peter Z
2015-01-01
The technique of site-directed spin labeling (SDSL) provides unique information on biomolecules by monitoring the behavior of a stable radical tag (i.e., spin label) using electron paramagnetic resonance (EPR) spectroscopy. In this chapter, we describe an approach in which SDSL is integrated with computational modeling to map conformations of nucleic acids. This approach builds upon a SDSL tool kit previously developed and validated, which includes three components: (i) a nucleotide-independent nitroxide probe, designated as R5, which can be efficiently attached at defined sites within arbitrary nucleic acid sequences; (ii) inter-R5 distances in the nanometer range, measured via pulsed EPR; and (iii) an efficient program, called NASNOX, that computes inter-R5 distances on given nucleic acid structures. Following a general framework of data mining, our approach uses multiple sets of measured inter-R5 distances to retrieve "correct" all-atom models from a large ensemble of models. The pool of models can be generated independently without relying on the inter-R5 distances, thus allowing a large degree of flexibility in integrating the SDSL-measured distances with a modeling approach best suited for the specific system under investigation. As such, the integrative experimental/computational approach described here represents a hybrid method for determining all-atom models based on experimentally-derived distance measurements. PMID:26477260
Bayesian approaches to spatial inference: Modelling and computational challenges and solutions
NASA Astrophysics Data System (ADS)
Moores, Matthew; Mengersen, Kerrie
2014-12-01
We discuss a range of Bayesian modelling approaches for spatial data and investigate some of the associated computational challenges. This paper commences with a brief review of Bayesian mixture models and Markov random fields, with enabling computational algorithms including Markov chain Monte Carlo (MCMC) and integrated nested Laplace approximation (INLA). Following this, we focus on the Potts model as a canonical approach, and discuss the challenge of estimating the inverse temperature parameter that controls the degree of spatial smoothing. We compare three approaches to addressing the doubly intractable nature of the likelihood, namely pseudo-likelihood, path sampling and the exchange algorithm. These techniques are applied to satellite data used to analyse water quality in the Great Barrier Reef.
A computational approach to continuum damping of Alfven waves in two and three-dimensional geometry
Koenies, Axel; Kleiber, Ralf
2012-12-15
While the usual way of calculating continuum damping of global Alfven modes is the introduction of a small artificial resistivity, we present a computational approach to the problem based on a suitable path of integration in the complex plane. This approach is implemented by the Riccati shooting method and it is shown that it can be transferred to the Galerkin method used in three-dimensional ideal magneto-hydrodynamics (MHD) codes. The new approach turns out to be less expensive with respect to resolution and computation time than the usual one. We present an application to large aspect ratio tokamak and stellarator equilibria retaining a few Fourier harmonics only and calculate eigenfunctions and continuum damping rates. These may serve as an input for kinetic MHD hybrid models making it possible to bypass the problem of having singularities on the path of integration on one hand and considering continuum damping on the other.
NASA Astrophysics Data System (ADS)
Salehi, Mohammad Reza; Abiri, Ebrahim; Dehyadegari, Louiza
2013-10-01
This paper seeks to investigate an approach of photonic reservoir computing for optical speech recognition on an examination isolated digit recognition task. An analytical approach in photonic reservoir computing is further drawn on to decrease time consumption, compared to numerical methods; which is very important in processing large signals such as speech recognition. It is also observed that adjusting reservoir parameters along with a good nonlinear mapping of the input signal into the reservoir, analytical approach, would boost recognition accuracy performance. Perfect recognition accuracy (i.e. 100%) can be achieved for noiseless speech signals. For noisy signals with 0-10 db of signal to noise ratios, however, the accuracy ranges observed varied between 92% and 98%. In fact, photonic reservoir application demonstrated 9-18% improvement compared to classical reservoir networks with hyperbolic tangent nodes.
Viscous-inviscid interaction computations using a pseudo Navier-Stokes approach
NASA Technical Reports Server (NTRS)
Whitfield, D. L.
1985-01-01
A new method is presented for the computation of viscous-inviscid interaction. The idea is to treat rotational inviscid flow (of which flows are almost entirely composed) in a thorough manner, and accept an approximation treatment of vorticity as introduced by viscous effects. The approach is to numerically solve the Navier-Stokes equations with the viscous terms determined from an inverse boundary-layer solution. The method falls somewhere between a Navier-Stokes approach and an Euler and boundary-layer equation coupling approach; consequently, it is referred to as a pseudo Navier-Stokes approach. Results from both the Navier-Stokes equations and the pseudo Navier-Stokes approach are presented.
Accurate basis set truncation for wavefunction embedding
NASA Astrophysics Data System (ADS)
Barnes, Taylor A.; Goodpaster, Jason D.; Manby, Frederick R.; Miller, Thomas F.
2013-07-01
Density functional theory (DFT) provides a formally exact framework for performing embedded subsystem electronic structure calculations, including DFT-in-DFT and wavefunction theory-in-DFT descriptions. In the interest of efficiency, it is desirable to truncate the atomic orbital basis set in which the subsystem calculation is performed, thus avoiding high-order scaling with respect to the size of the MO virtual space. In this study, we extend a recently introduced projection-based embedding method [F. R. Manby, M. Stella, J. D. Goodpaster, and T. F. Miller III, J. Chem. Theory Comput. 8, 2564 (2012)], 10.1021/ct300544e to allow for the systematic and accurate truncation of the embedded subsystem basis set. The approach is applied to both covalently and non-covalently bound test cases, including water clusters and polypeptide chains, and it is demonstrated that errors associated with basis set truncation are controllable to well within chemical accuracy. Furthermore, we show that this approach allows for switching between accurate projection-based embedding and DFT embedding with approximate kinetic energy (KE) functionals; in this sense, the approach provides a means of systematically improving upon the use of approximate KE functionals in DFT embedding.
A computational study of thrust augmenting ejectors based on a viscous-inviscid approach
NASA Astrophysics Data System (ADS)
Lund, Thomas Scott
Today's VSTOL designer is in need of an accurate theoretical model that can swiftly evaluate various ejector configurations. A viscous-inviscid interaction technique is advocated as both an efficient and accurate means of predicting the performance of two-dimensional thrust augmenting ejectors. The flowfield is divided into a viscous region that contains the turbulent jet, and an inviscid region that contains the ambient fluid drawn into the device. The inviscid region is computed with a higher order panel method, while an integral method is used for the description of the viscous part. The strong viscous-inviscid interaction present within the injector is simulated in an iterative process where two regions influence each other en route to a converged solution. This formulation retains much of the essential physics of the problem, but at the same time requires only a small amount of computing effort. The model is applied to a variety of parametric and optimization studies involving ejectors having either one or two primary jets. In all cases, it was found that the dual-jet ejector out performs its single jet counterpart. This fact is attributed to enhanced mixing due to an increase in effective ejector length.
A computer vision approach for solar radiation nowcasting using MSG images
NASA Astrophysics Data System (ADS)
Álvarez, L.; Castaño Moraga, C. A.; Martín, J.
2010-09-01
Cloud structures and haze are the two main atmospheric phenomena that reduce the performance of solar power plants, since they absorb solar energy reaching terrestrial surface. Thus, accurate forecasting of solar radiation is a challenging research area that involves both a precise localization of cloud structures and haze, as well as the attenuation introduced by these artifacts. Our work presents a novel approach for nowcasting services based on image processing techniques applied to MSG satellite images provided by the EUMETSAT Rapid Scan Service (RSS) service. These data are an interesting source of information for our purposes since every 5 minutes we obtain actual information of the atmospheric state in nearly real time. However, a workaround must be given in order to forecast solar radiation. To that end, we synthetically forecast MSG images forecasts from past images applying computer vision techniques adapted to fluid flows in order to evolve atmospheric state. First, we classify cloud structures on two different layers, corresponding to top and bottom clouds, which includes haze. This two-level classification responds to the dominant climate conditions found in our region of interest, the Canary Islands archipelago, regulated by the Gulf Stream and Trade Winds. Vertical structure of Trade Winds consists of two layers, the bottom one, which is fresh and humid, and the top one, which is warm and dry. Between these two layers a thermal inversion appears that does not allow bottom clouds to go up and naturally divides clouds in these two layers. Top clouds can be directly obtained from satellite images by means of a segmentation algorithm on histogram heights. However, bottom clouds are usually overlapped by the former, so an inpainting algorithm is used to recover overlapped areas of bottom clouds. For each layer, cloud motion is estimated through a correlation based optic flow algorithm that provides a vector field that describes the displacement field in
Toward a computational approach for collision avoidance with real-world scenes
NASA Astrophysics Data System (ADS)
Keil, Matthias S.; Rodriguez-Vazquez, Angel
2003-04-01
In the central nervous systems of animals like pigeons and locusts, neurons were identified which signal objects approaching the animal on a direct collision course. In order to timely initiate escape behavior, these neurons must recognize a possible approach (or at least differentiate it from similar but non-threatening situations), and estimate the time-to-collision (ttc). Unraveling the neural circuitry for collision avoidance, and identifying the underlying computational principles, should thus be promising for building vision-based neuromorphic architectures, which in the near future could find applications in cars or planes. Unfortunately, a corresponding computational architecture which is able to handle real-situations (e.g. moving backgrounds, different lighting conditions) is still not available (successful collision avoidance of a robot was demonstrated only for a closed environment). Here we present two computational models for signalling impending collision. These models are parsimonious since they possess only the minimum number of computational units which are essential to reproduce corresponding biological data. Our models show robust performance in adverse situations, such as with approaching low-contrast objects, or with highly textured backgrounds. Furthermore, a condition is proposed under which the responses of our models match the so-called eta-function. We finally discuss which components need to be added to our model to convert it into a full-fledged real-world-environment collision detector.